                                   showdb


Wiki

   The master copies of EMBOSS documentation are available at
   http://emboss.open-bio.org/wiki/Appdocs on the EMBOSS Wiki.

   Please help by correcting and extending the Wiki pages.

Function

   Display information on configured databases

Description

   showdb displays a table with the names, contents and access methods of
   the sequence databases configured for your EMBOSS installation.

Usage

   Here is a sample session with showdb

   Display information on the currently available databases:

% showdb
Display information on configured databases

# Name            Type                          Comment
# =============== ============================= =======
bpsw              Protein,Protfeatures          BioPerl OBDA index of test Swiss
Prot
bpworm            Protein                       BioPerl OBDA index of test wormp
ep fasta file
qapblast          Protein                       BLAST swissnew
qapblastall       Protein                       BLAST swissnew, all fields index
ed
qapblastsplit     Protein                       BLAST swissnew split in 5 files
qapblastsplitexc  Protein                       BLAST swissnew split in 5 files,
 not file 02
qapblastsplitinc  Protein                       BLAST swissnew split in 5 files,
 only file 02
qapfasta          Protein                       FASTA file swissnew entries
qapflat           Protein,Protfeatures          SpTrEmbl flatfile
qapflatall        Protein,Protfeatures          SpTrEmbl flatfiles, all fields i
ndexed
qapir             Protein,Protfeatures          Test PIR indexed by dbigcg
qapirall          Protein,Protfeatures          Test PIR indexed by dbigcg with
fields
qapirexc          Protein,Protfeatures          Test PIR indexed by dbigcg excep
t file pir1
qapirinc          Protein,Protfeatures          Test PIR indexed by dbigcg file
pir1
qapxfasta         Protein                       FASTA file swissnew entries
qapxflat          Protein                       Swissnew flatfiles
qasrswww          Protein,Protfeatures          Remote SRS web server
qaxpir            Protein,Protfeatures          PIR indexed by dbxgcg
qaxpirall         Protein,Protfeatures          Test PIR indexed by dbxgcg with
fields
qaxpirexc         Protein,Protfeatures          Test PIR indexed by dbxgcg excep
t pir1
qaxpirinc         Protein,Protfeatures          Test PIR indexed by dbxgcg file
pir1
tpir              Protein                       Test PIR using NBRF access for 4
 files
tsw               Protein,Protfeatures,Text     Swissprot native format with EMB
L CD-ROM index
tswnew            Protein,Protfeatures          SpTrEmbl as 3 files in native fo
rmat with EMBL CD-ROM index
bpembl            Nucleotide,Nucfeatures        BioPerl OBDA index of test EMBL
bpgb              Nucleotide,Nucfeatures        BioPerl OBDA index of test GenBa
nk
ena               Nucleotide,Nucfeatures        ENA via URL
qanfasta          Nucleotide                    FASTA file EMBL rodents
qanfastaall       Nucleotide                    FASTA file EMBL rodents, all fie
lds indexed
qanflat           Nucleotide,Nucfeatures,Refseq EMBL flatfiles
qanflatall        Nucleotide,Nucfeatures,Refseq EMBL flatfiles
qanflatexc        Nucleotide,Nucfeatures        EMBL flatfiles, no rodent file
qanflatinc        Nucleotide,Nucfeatures        EMBL flatfiles, only rodent file
qangcg            Nucleotide,Nucfeatures        GCG format test EMBL
qangcgall         Nucleotide,Nucfeatures        GCG format test EMBL
qangcgexc         Nucleotide,Nucfeatures        GCG format test EMBL without pro
karyotes
qangcginc         Nucleotide,Nucfeatures        GCG format test EMBL only prokar
yotes
qanxfasta         Nucleotide                    FASTA file EMBL rodents
qanxfastaall      Nucleotide                    FASTA file EMBL rodents, all fie
lds indexed
qanxflat          Nucleotide,Nucfeatures,Refseq EMBL flatfiles
qanxflatall       Nucleotide,Nucfeatures,Refseq EMBL flatfiles, all fields index
ed
qanxflatexc       Nucleotide,Nucfeatures,Refseq EMBL flatfiles, no rodent file
qanxflatinc       Nucleotide,Nucfeatures        EMBL flatfiles, only rodent file
qanxgcg           Nucleotide,Nucfeatures        GCG format EMBL
qanxgcgall        Nucleotide,Nucfeatures        GCG format EMBL indexed by dbxgc
g with query fields
qanxgcgexc        Nucleotide,Nucfeatures        GCG format EMBL without prokaryo
tes
qanxgcginc        Nucleotide,Nucfeatures        GCG format EMBL only prokaryotes
qawfasta          Nucleotide                    FASTA file wormpep entries
qawxfasta         Nucleotide                    FASTA file wormpep entries
qaxembl           Nucleotide,Nucfeatures,Refseq EMBL flatfiles
tembl             Nucleotide,Refseq,Nucfeatures EMBL in native format with EMBL
CD-ROM index
temblall          Nucleotide,Nucfeatures,Refseq EMBL in native format with EMBL
CD-ROM index
temblrest         Nucleotide,Nucfeatures,Refseq EMBL in native format with EMBL
CD-ROM index
temblvrt          Nucleotide,Nucfeatures        EMBL in native format with EMBL
CD-ROM index
tensembldasgrch37 Nucleotide                    Homo_sapiens Reference server ba
sed on GRCh37 assembly
testdb            Nucleotide                    test sequence data
tgb               Nucleotide,Nucfeatures        Genbank by SRS at DKFZ
tgenbank          Nucleotide,Nucfeatures        Test GenBank in native format wi
th EMBL CD-ROM index
tgenedashuman     Nucleotide                    The Ensembl human Gene_ID refere
nce source
tflybase          Features                      Flybase CHADO server
tgenedb           Features                      GeneDb CHADO server
ttax              Taxonomy                      NCBI taxonomy test data
taxon             Taxonomy                      NCBI taxonomy
drcat             Resource                      Data Resource Catalogue
tedam             Obo                           Test EDAM using dbxedam test ind
exes
tobo              Obo                           Test EDAM using dbxobo test inde
xes
chebi             Obo                           Chemical Entities of Biological
Interest
eco               Obo                           Evidence code ontology
edam              Obo                           EMBRACE Data and Methods ontolog
y
edam_data         Obo                           EMBRACE Data and Methods ontolog
y (data)
edam_format       Obo                           EMBRACE Data and Methods ontolog
y (formats)
edam_identifier   Obo                           EMBRACE Data and Methods ontolog
y (identifiers)
edam_operation    Obo                           EMBRACE Data and Methods ontolog
y (operations)
edam_topic        Obo                           EMBRACE Data and Methods ontolog
y (topics)
go                Obo                           Gene Ontology
go_component      Obo                           Gene Ontology (cellular componen
ts)
go_function       Obo                           Gene Ontology (molecular functio
ns)
go_process        Obo                           Gene Ontology (biological proces
ses)
pw                Obo                           Pathways ontology
ro                Obo                           Relations ontology
so                Obo                           Sequence ontology
swo               Obo                           Software ontology

   Example 2

   Write the results to a file:

% showdb -outfile showdb.out
Display information on configured databases

   Go to the output files for this example

   Example 3

   Display information on one explicit database:

% showdb -database tsw
Display information on configured databases

# Name         Type                      Comment
# ============ ========================= =======
tsw            Protein,Protfeatures,Text Swissprot native format with EMBL CD-RO
M index

   Go to the input files for this example

   Example 4

   Display information on the databases formatted in HTML:

% showdb -html
Display information on configured databases

 Name Type Comment

 bpsw Protein Protfeatures BioPerl OBDA index of test SwissProt

 bpworm Protein BioPerl OBDA index of test wormpep fasta file

 qapblast Protein BLAST swissnew

 qapblastall Protein BLAST swissnew, all fields indexed

 qapblastsplit Protein BLAST swissnew split in 5 files

 qapblastsplitexc Protein BLAST swissnew split in 5 files, not file 02

 qapblastsplitinc Protein BLAST swissnew split in 5 files, only file 02

 qapfasta Protein FASTA file swissnew entries

 qapflat Protein Protfeatures SpTrEmbl flatfile

 qapflatall Protein Protfeatures SpTrEmbl flatfiles, all fields indexed

 qapir Protein Protfeatures Test PIR indexed by dbigcg

 qapirall Protein Protfeatures Test PIR indexed by dbigcg with fields

 qapirexc Protein Protfeatures Test PIR indexed by dbigcg except file pir1

 qapirinc Protein Protfeatures Test PIR indexed by dbigcg file pir1

 qapxfasta Protein FASTA file swissnew entries

 qapxflat Protein Swissnew flatfiles

 qasrswww Protein Protfeatures Remote SRS web server

 qaxpir Protein Protfeatures PIR indexed by dbxgcg

 qaxpirall Protein Protfeatures Test PIR indexed by dbxgcg with fields

 qaxpirexc Protein Protfeatures Test PIR indexed by dbxgcg except pir1

 qaxpirinc Protein Protfeatures Test PIR indexed by dbxgcg file pir1

 tpir Protein Test PIR using NBRF access for 4 files

 tsw Protein Protfeatures Text Swissprot native format with EMBL CD-ROM index

 tswnew Protein Protfeatures SpTrEmbl as 3 files in native format with EMBL CD-R
OM index

 bpembl Nucleotide Nucfeatures BioPerl OBDA index of test EMBL

 bpgb Nucleotide Nucfeatures BioPerl OBDA index of test GenBank

 ena Nucleotide Nucfeatures ENA via URL

 qanfasta Nucleotide FASTA file EMBL rodents

 qanfastaall Nucleotide FASTA file EMBL rodents, all fields indexed

 qanflat Nucleotide Nucfeatures Refseq EMBL flatfiles

 qanflatall Nucleotide Nucfeatures Refseq EMBL flatfiles

 qanflatexc Nucleotide Nucfeatures EMBL flatfiles, no rodent file

 qanflatinc Nucleotide Nucfeatures EMBL flatfiles, only rodent file

 qangcg Nucleotide Nucfeatures GCG format test EMBL

 qangcgall Nucleotide Nucfeatures GCG format test EMBL

 qangcgexc Nucleotide Nucfeatures GCG format test EMBL without prokaryotes

 qangcginc Nucleotide Nucfeatures GCG format test EMBL only prokaryotes

 qanxfasta Nucleotide FASTA file EMBL rodents

 qanxfastaall Nucleotide FASTA file EMBL rodents, all fields indexed

 qanxflat Nucleotide Nucfeatures Refseq EMBL flatfiles

 qanxflatall Nucleotide Nucfeatures Refseq EMBL flatfiles, all fields indexed

 qanxflatexc Nucleotide Nucfeatures Refseq EMBL flatfiles, no rodent file

 qanxflatinc Nucleotide Nucfeatures EMBL flatfiles, only rodent file

 qanxgcg Nucleotide Nucfeatures GCG format EMBL

 qanxgcgall Nucleotide Nucfeatures GCG format EMBL indexed by dbxgcg with query
fields

 qanxgcgexc Nucleotide Nucfeatures GCG format EMBL without prokaryotes

 qanxgcginc Nucleotide Nucfeatures GCG format EMBL only prokaryotes

 qawfasta Nucleotide FASTA file wormpep entries

 qawxfasta Nucleotide FASTA file wormpep entries

 qaxembl Nucleotide Nucfeatures Refseq EMBL flatfiles

 tembl Nucleotide Refseq Nucfeatures EMBL in native format with EMBL CD-ROM inde
x

 temblall Nucleotide Nucfeatures Refseq EMBL in native format with EMBL CD-ROM i
ndex

 temblrest Nucleotide Nucfeatures Refseq EMBL in native format with EMBL CD-ROM
index

 temblvrt Nucleotide Nucfeatures EMBL in native format with EMBL CD-ROM index

 tensembldasgrch37 Nucleotide Homo_sapiens Reference server based on GRCh37 asse
mbly

 testdb Nucleotide test sequence data

 tgb Nucleotide Nucfeatures Genbank by SRS at DKFZ

 tgenbank Nucleotide Nucfeatures Test GenBank in native format with EMBL CD-ROM
index

 tgenedashuman Nucleotide The Ensembl human Gene_ID reference source

 tflybase Features Flybase CHADO server

 tgenedb Features GeneDb CHADO server

 ttax Taxonomy NCBI taxonomy test data

 taxon Taxonomy NCBI taxonomy

 drcat Resource Data Resource Catalogue

 tedam Obo Test EDAM using dbxedam test indexes

 tobo Obo Test EDAM using dbxobo test indexes

 chebi Obo Chemical Entities of Biological Interest

 eco Obo Evidence code ontology

 edam Obo EMBRACE Data and Methods ontology

 edam_data Obo EMBRACE Data and Methods ontology (data)

 edam_format Obo EMBRACE Data and Methods ontology (formats)

 edam_identifier Obo EMBRACE Data and Methods ontology (identifiers)

 edam_operation Obo EMBRACE Data and Methods ontology (operations)

 edam_topic Obo EMBRACE Data and Methods ontology (topics)

 go Obo Gene Ontology

 go_component Obo Gene Ontology (cellular components)

 go_function Obo Gene Ontology (molecular functions)

 go_process Obo Gene Ontology (biological processes)

 pw Obo Pathways ontology

 ro Obo Relations ontology

 so Obo Sequence ontology

 swo Obo Software ontology

   Example 5

   Display protein databases only:

% showdb -nonucleic
Display information on configured databases

# Name            Type                          Comment
# =============== ============================= =======
bpsw              Protein,Protfeatures          BioPerl OBDA index of test Swiss
Prot
bpworm            Protein                       BioPerl OBDA index of test wormp
ep fasta file
qapblast          Protein                       BLAST swissnew
qapblastall       Protein                       BLAST swissnew, all fields index
ed
qapblastsplit     Protein                       BLAST swissnew split in 5 files
qapblastsplitexc  Protein                       BLAST swissnew split in 5 files,
 not file 02
qapblastsplitinc  Protein                       BLAST swissnew split in 5 files,
 only file 02
qapfasta          Protein                       FASTA file swissnew entries
qapflat           Protein,Protfeatures          SpTrEmbl flatfile
qapflatall        Protein,Protfeatures          SpTrEmbl flatfiles, all fields i
ndexed
qapir             Protein,Protfeatures          Test PIR indexed by dbigcg
qapirall          Protein,Protfeatures          Test PIR indexed by dbigcg with
fields
qapirexc          Protein,Protfeatures          Test PIR indexed by dbigcg excep
t file pir1
qapirinc          Protein,Protfeatures          Test PIR indexed by dbigcg file
pir1
qapxfasta         Protein                       FASTA file swissnew entries
qapxflat          Protein                       Swissnew flatfiles
qasrswww          Protein,Protfeatures          Remote SRS web server
qaxpir            Protein,Protfeatures          PIR indexed by dbxgcg
qaxpirall         Protein,Protfeatures          Test PIR indexed by dbxgcg with
fields
qaxpirexc         Protein,Protfeatures          Test PIR indexed by dbxgcg excep
t pir1
qaxpirinc         Protein,Protfeatures          Test PIR indexed by dbxgcg file
pir1
tpir              Protein                       Test PIR using NBRF access for 4
 files
tsw               Protein,Protfeatures,Text     Swissprot native format with EMB
L CD-ROM index
tswnew            Protein,Protfeatures          SpTrEmbl as 3 files in native fo
rmat with EMBL CD-ROM index
tflybase          Features                      Flybase CHADO server
tgenedb           Features                      GeneDb CHADO server
ttax              Taxonomy                      NCBI taxonomy test data
taxon             Taxonomy                      NCBI taxonomy
drcat             Resource                      Data Resource Catalogue
tedam             Obo                           Test EDAM using dbxedam test ind
exes
tobo              Obo                           Test EDAM using dbxobo test inde
xes
chebi             Obo                           Chemical Entities of Biological
Interest
eco               Obo                           Evidence code ontology
edam              Obo                           EMBRACE Data and Methods ontolog
y
edam_data         Obo                           EMBRACE Data and Methods ontolog
y (data)
edam_format       Obo                           EMBRACE Data and Methods ontolog
y (formats)
edam_identifier   Obo                           EMBRACE Data and Methods ontolog
y (identifiers)
edam_operation    Obo                           EMBRACE Data and Methods ontolog
y (operations)
edam_topic        Obo                           EMBRACE Data and Methods ontolog
y (topics)
go                Obo                           Gene Ontology
go_component      Obo                           Gene Ontology (cellular componen
ts)
go_function       Obo                           Gene Ontology (molecular functio
ns)
go_process        Obo                           Gene Ontology (biological proces
ses)
pw                Obo                           Pathways ontology
ro                Obo                           Relations ontology
so                Obo                           Sequence ontology
swo               Obo                           Software ontology

   Example 6

   Display the information with no headings:

% showdb -noheading
Display information on configured databases

bpsw              Protein,Protfeatures          BioPerl OBDA index of test Swiss
Prot
bpworm            Protein                       BioPerl OBDA index of test wormp
ep fasta file
qapblast          Protein                       BLAST swissnew
qapblastall       Protein                       BLAST swissnew, all fields index
ed
qapblastsplit     Protein                       BLAST swissnew split in 5 files
qapblastsplitexc  Protein                       BLAST swissnew split in 5 files,
 not file 02
qapblastsplitinc  Protein                       BLAST swissnew split in 5 files,
 only file 02
qapfasta          Protein                       FASTA file swissnew entries
qapflat           Protein,Protfeatures          SpTrEmbl flatfile
qapflatall        Protein,Protfeatures          SpTrEmbl flatfiles, all fields i
ndexed
qapir             Protein,Protfeatures          Test PIR indexed by dbigcg
qapirall          Protein,Protfeatures          Test PIR indexed by dbigcg with
fields
qapirexc          Protein,Protfeatures          Test PIR indexed by dbigcg excep
t file pir1
qapirinc          Protein,Protfeatures          Test PIR indexed by dbigcg file
pir1
qapxfasta         Protein                       FASTA file swissnew entries
qapxflat          Protein                       Swissnew flatfiles
qasrswww          Protein,Protfeatures          Remote SRS web server
qaxpir            Protein,Protfeatures          PIR indexed by dbxgcg
qaxpirall         Protein,Protfeatures          Test PIR indexed by dbxgcg with
fields
qaxpirexc         Protein,Protfeatures          Test PIR indexed by dbxgcg excep
t pir1
qaxpirinc         Protein,Protfeatures          Test PIR indexed by dbxgcg file
pir1
tpir              Protein                       Test PIR using NBRF access for 4
 files
tsw               Protein,Protfeatures,Text     Swissprot native format with EMB
L CD-ROM index
tswnew            Protein,Protfeatures          SpTrEmbl as 3 files in native fo
rmat with EMBL CD-ROM index
bpembl            Nucleotide,Nucfeatures        BioPerl OBDA index of test EMBL
bpgb              Nucleotide,Nucfeatures        BioPerl OBDA index of test GenBa
nk
ena               Nucleotide,Nucfeatures        ENA via URL
qanfasta          Nucleotide                    FASTA file EMBL rodents
qanfastaall       Nucleotide                    FASTA file EMBL rodents, all fie
lds indexed
qanflat           Nucleotide,Nucfeatures,Refseq EMBL flatfiles
qanflatall        Nucleotide,Nucfeatures,Refseq EMBL flatfiles
qanflatexc        Nucleotide,Nucfeatures        EMBL flatfiles, no rodent file
qanflatinc        Nucleotide,Nucfeatures        EMBL flatfiles, only rodent file
qangcg            Nucleotide,Nucfeatures        GCG format test EMBL
qangcgall         Nucleotide,Nucfeatures        GCG format test EMBL
qangcgexc         Nucleotide,Nucfeatures        GCG format test EMBL without pro
karyotes
qangcginc         Nucleotide,Nucfeatures        GCG format test EMBL only prokar
yotes
qanxfasta         Nucleotide                    FASTA file EMBL rodents
qanxfastaall      Nucleotide                    FASTA file EMBL rodents, all fie
lds indexed
qanxflat          Nucleotide,Nucfeatures,Refseq EMBL flatfiles
qanxflatall       Nucleotide,Nucfeatures,Refseq EMBL flatfiles, all fields index
ed
qanxflatexc       Nucleotide,Nucfeatures,Refseq EMBL flatfiles, no rodent file
qanxflatinc       Nucleotide,Nucfeatures        EMBL flatfiles, only rodent file
qanxgcg           Nucleotide,Nucfeatures        GCG format EMBL
qanxgcgall        Nucleotide,Nucfeatures        GCG format EMBL indexed by dbxgc
g with query fields
qanxgcgexc        Nucleotide,Nucfeatures        GCG format EMBL without prokaryo
tes
qanxgcginc        Nucleotide,Nucfeatures        GCG format EMBL only prokaryotes
qawfasta          Nucleotide                    FASTA file wormpep entries
qawxfasta         Nucleotide                    FASTA file wormpep entries
qaxembl           Nucleotide,Nucfeatures,Refseq EMBL flatfiles
tembl             Nucleotide,Refseq,Nucfeatures EMBL in native format with EMBL
CD-ROM index
temblall          Nucleotide,Nucfeatures,Refseq EMBL in native format with EMBL
CD-ROM index
temblrest         Nucleotide,Nucfeatures,Refseq EMBL in native format with EMBL
CD-ROM index
temblvrt          Nucleotide,Nucfeatures        EMBL in native format with EMBL
CD-ROM index
tensembldasgrch37 Nucleotide                    Homo_sapiens Reference server ba
sed on GRCh37 assembly
testdb            Nucleotide                    test sequence data
tgb               Nucleotide,Nucfeatures        Genbank by SRS at DKFZ
tgenbank          Nucleotide,Nucfeatures        Test GenBank in native format wi
th EMBL CD-ROM index
tgenedashuman     Nucleotide                    The Ensembl human Gene_ID refere
nce source
tflybase          Features                      Flybase CHADO server
tgenedb           Features                      GeneDb CHADO server
ttax              Taxonomy                      NCBI taxonomy test data
taxon             Taxonomy                      NCBI taxonomy
drcat             Resource                      Data Resource Catalogue
tedam             Obo                           Test EDAM using dbxedam test ind
exes
tobo              Obo                           Test EDAM using dbxobo test inde
xes
chebi             Obo                           Chemical Entities of Biological
Interest
eco               Obo                           Evidence code ontology
edam              Obo                           EMBRACE Data and Methods ontolog
y
edam_data         Obo                           EMBRACE Data and Methods ontolog
y (data)
edam_format       Obo                           EMBRACE Data and Methods ontolog
y (formats)
edam_identifier   Obo                           EMBRACE Data and Methods ontolog
y (identifiers)
edam_operation    Obo                           EMBRACE Data and Methods ontolog
y (operations)
edam_topic        Obo                           EMBRACE Data and Methods ontolog
y (topics)
go                Obo                           Gene Ontology
go_component      Obo                           Gene Ontology (cellular componen
ts)
go_function       Obo                           Gene Ontology (molecular functio
ns)
go_process        Obo                           Gene Ontology (biological proces
ses)
pw                Obo                           Pathways ontology
ro                Obo                           Relations ontology
so                Obo                           Sequence ontology
swo               Obo                           Software ontology

   Example 7

   Display just a list of the available database names:

% showdb -noheading -notype -noid -noquery -noall -nocomment -auto

bpsw
bpworm
qapblast
qapblastall
qapblastsplit
qapblastsplitexc
qapblastsplitinc
qapfasta
qapflat
qapflatall
qapir
qapirall
qapirexc
qapirinc
qapxfasta
qapxflat
qasrswww
qaxpir
qaxpirall
qaxpirexc
qaxpirinc
tpir
tsw
tswnew
bpembl
bpgb
ena
qanfasta
qanfastaall
qanflat
qanflatall
qanflatexc
qanflatinc
qangcg
qangcgall
qangcgexc
qangcginc
qanxfasta
qanxfastaall
qanxflat
qanxflatall
qanxflatexc
qanxflatinc
qanxgcg
qanxgcgall
qanxgcgexc
qanxgcginc
qawfasta
qawxfasta
qaxembl
tembl
temblall
temblrest
temblvrt
tensembldasgrch37
testdb
tgb
tgenbank
tgenedashuman
tflybase
tgenedb
ttax
taxon
drcat
tedam
tobo
chebi
eco
edam
edam_data
edam_format
edam_identifier
edam_operation
edam_topic
go
go_component
go_function
go_process
pw
ro
so
swo

   Example 8

   Display only the names and types:

% showdb -only -type
Display information on configured databases

bpsw              Protein,Protfeatures
bpworm            Protein
qapblast          Protein
qapblastall       Protein
qapblastsplit     Protein
qapblastsplitexc  Protein
qapblastsplitinc  Protein
qapfasta          Protein
qapflat           Protein,Protfeatures
qapflatall        Protein,Protfeatures
qapir             Protein,Protfeatures
qapirall          Protein,Protfeatures
qapirexc          Protein,Protfeatures
qapirinc          Protein,Protfeatures
qapxfasta         Protein
qapxflat          Protein
qasrswww          Protein,Protfeatures
qaxpir            Protein,Protfeatures
qaxpirall         Protein,Protfeatures
qaxpirexc         Protein,Protfeatures
qaxpirinc         Protein,Protfeatures
tpir              Protein
tsw               Protein,Protfeatures,Text
tswnew            Protein,Protfeatures
bpembl            Nucleotide,Nucfeatures
bpgb              Nucleotide,Nucfeatures
ena               Nucleotide,Nucfeatures
qanfasta          Nucleotide
qanfastaall       Nucleotide
qanflat           Nucleotide,Nucfeatures,Refseq
qanflatall        Nucleotide,Nucfeatures,Refseq
qanflatexc        Nucleotide,Nucfeatures
qanflatinc        Nucleotide,Nucfeatures
qangcg            Nucleotide,Nucfeatures
qangcgall         Nucleotide,Nucfeatures
qangcgexc         Nucleotide,Nucfeatures
qangcginc         Nucleotide,Nucfeatures
qanxfasta         Nucleotide
qanxfastaall      Nucleotide
qanxflat          Nucleotide,Nucfeatures,Refseq
qanxflatall       Nucleotide,Nucfeatures,Refseq
qanxflatexc       Nucleotide,Nucfeatures,Refseq
qanxflatinc       Nucleotide,Nucfeatures
qanxgcg           Nucleotide,Nucfeatures
qanxgcgall        Nucleotide,Nucfeatures
qanxgcgexc        Nucleotide,Nucfeatures
qanxgcginc        Nucleotide,Nucfeatures
qawfasta          Nucleotide
qawxfasta         Nucleotide
qaxembl           Nucleotide,Nucfeatures,Refseq
tembl             Nucleotide,Refseq,Nucfeatures
temblall          Nucleotide,Nucfeatures,Refseq
temblrest         Nucleotide,Nucfeatures,Refseq
temblvrt          Nucleotide,Nucfeatures
tensembldasgrch37 Nucleotide
testdb            Nucleotide
tgb               Nucleotide,Nucfeatures
tgenbank          Nucleotide,Nucfeatures
tgenedashuman     Nucleotide
tflybase          Features
tgenedb           Features
ttax              Taxonomy
taxon             Taxonomy
drcat             Resource
tedam             Obo
tobo              Obo
chebi             Obo
eco               Obo
edam              Obo
edam_data         Obo
edam_format       Obo
edam_identifier   Obo
edam_operation    Obo
edam_topic        Obo
go                Obo
go_component      Obo
go_function       Obo
go_process        Obo
pw                Obo
ro                Obo
so                Obo
swo               Obo

   Example 9

   Display everything

% showdb -full
Display information on configured databases

# Name            Type                          ID  Qry All Method    Taxon
                  Fields
                                        Aliases         Examples           Defin
ed  Release             Comment
# =============== ============================= ==  === === ========= ==========
================= ==============================================================
======================================= =============== ================== =====
=== =================== =======
bpsw              Protein,Protfeatures          OK  OK  OK  obda      -
                       2 id,acc
                                              0 -              0 -         speci
al                      BioPerl OBDA index of test SwissProt
bpworm            Protein                       OK  OK  OK  obda      -
                       1 id
                                              0 -              0 -         speci
al                      BioPerl OBDA index of test wormpep fasta file
qapblast          Protein                       OK  OK  OK  blast     1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      BLAST swissnew
qapblastall       Protein                       OK  OK  OK  blast     1_all
                       4 sv,des
                                              0 -              0 -         speci
al                      BLAST swissnew, all fields indexed
qapblastsplit     Protein                       OK  OK  OK  blast     1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      BLAST swissnew split in 5 files
qapblastsplitexc  Protein                       OK  OK  OK  blast     1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      BLAST swissnew split in 5 files, not file 02
qapblastsplitinc  Protein                       OK  OK  OK  blast     1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      BLAST swissnew split in 5 files, only file 02
qapfasta          Protein                       OK  OK  OK  emblcd    1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      FASTA file swissnew entries
qapflat           Protein,Protfeatures          OK  OK  OK  emblcd    1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      SpTrEmbl flatfile
qapflatall        Protein,Protfeatures          OK  OK  OK  emblcd    1_all
                       6 sv,des,org,key
                                              0 -              0 -         speci
al                      SpTrEmbl flatfiles, all fields indexed
qapir             Protein,Protfeatures          OK  OK  OK  gcg       1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      Test PIR indexed by dbigcg
qapirall          Protein,Protfeatures          OK  OK  OK  gcg       1_all
                       5 des,org,key
                                              0 -              0 -         speci
al                      Test PIR indexed by dbigcg with fields
qapirexc          Protein,Protfeatures          OK  OK  OK  gcg       1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      Test PIR indexed by dbigcg except file pir1
qapirinc          Protein,Protfeatures          OK  OK  OK  gcg       1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      Test PIR indexed by dbigcg file pir1
qapxfasta         Protein                       OK  OK  OK  emboss    1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      FASTA file swissnew entries
qapxflat          Protein                       OK  OK  OK  emboss    1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      Swissnew flatfiles
qasrswww          Protein,Protfeatures          OK  OK  OK  srswww    1_all
                       6 sv,des,org,key
                                              0 -              0 -         speci
al                      Remote SRS web server
qaxpir            Protein,Protfeatures          OK  OK  OK  embossgcg 1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      PIR indexed by dbxgcg
qaxpirall         Protein,Protfeatures          OK  OK  OK  embossgcg 1_all
                       5 des,org,key
                                              0 -              0 -         speci
al                      Test PIR indexed by dbxgcg with fields
qaxpirexc         Protein,Protfeatures          OK  OK  OK  embossgcg 1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      Test PIR indexed by dbxgcg except pir1
qaxpirinc         Protein,Protfeatures          OK  OK  OK  embossgcg 1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      Test PIR indexed by dbxgcg file pir1
tpir              Protein                       OK  OK  OK  gcg       1_all
                       5 des,org,key
                                              0 -              0 -         speci
al                      Test PIR using NBRF access for 4 files
tsw               Protein,Protfeatures,Text     OK  OK  OK  emblcd    1_all
                       6 id,acc,sv,des,org,key
                                              0 -              1 hba_human speci
al  36                  Swissprot native format with EMBL CD-ROM index
tswnew            Protein,Protfeatures          OK  OK  OK  emblcd    1_all
                       6 sv,des,org,key
                                              0 -              0 -         speci
al  37                  SpTrEmbl as 3 files in native format with EMBL CD-ROM in
dex
bpembl            Nucleotide,Nucfeatures        OK  OK  OK  obda      -
                       2 id,acc
                                              0 -              0 -         speci
al                      BioPerl OBDA index of test EMBL
bpgb              Nucleotide,Nucfeatures        OK  OK  OK  obda      -
                       2 id,acc
                                              0 -              0 -         speci
al                      BioPerl OBDA index of test GenBank
ena               Nucleotide,Nucfeatures        OK  OK  OK  url       1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      ENA via URL
qanfasta          Nucleotide                    OK  OK  OK  emblcd    9989_roden
tia                    2 id,acc
                                              0 -              0 -         speci
al                      FASTA file EMBL rodents
qanfastaall       Nucleotide                    OK  OK  OK  emblcd    9989_roden
tia                    4 sv,des
                                              0 -              0 -         speci
al                      FASTA file EMBL rodents, all fields indexed
qanflat           Nucleotide,Nucfeatures,Refseq OK  OK  OK  emblcd    1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      EMBL flatfiles
qanflatall        Nucleotide,Nucfeatures,Refseq OK  OK  OK  emblcd    1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      EMBL flatfiles
qanflatexc        Nucleotide,Nucfeatures        OK  OK  OK  emblcd    1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      EMBL flatfiles, no rodent file
qanflatinc        Nucleotide,Nucfeatures        OK  OK  OK  emblcd    -
                       2 id,acc
                                              0 -              0 -         speci
al                      EMBL flatfiles, only rodent file
qangcg            Nucleotide,Nucfeatures        OK  OK  OK  gcg       1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      GCG format test EMBL
qangcgall         Nucleotide,Nucfeatures        OK  OK  OK  gcg       1_all
                       6 sv,des,org,key
                                              0 -              0 -         speci
al                      GCG format test EMBL
qangcgexc         Nucleotide,Nucfeatures        OK  OK  OK  gcg       1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      GCG format test EMBL without prokaryotes
qangcginc         Nucleotide,Nucfeatures        OK  OK  OK  gcg       1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      GCG format test EMBL only prokaryotes
qanxfasta         Nucleotide                    OK  OK  OK  emboss    9989_roden
tia                    2 id,acc
                                              0 -              0 -         speci
al                      FASTA file EMBL rodents
qanxfastaall      Nucleotide                    OK  OK  OK  emboss    9989_roden
tia                    4 sv,des
                                              0 -              0 -         speci
al                      FASTA file EMBL rodents, all fields indexed
qanxflat          Nucleotide,Nucfeatures,Refseq OK  OK  OK  emboss    1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      EMBL flatfiles
qanxflatall       Nucleotide,Nucfeatures,Refseq OK  OK  OK  emboss    1_all
                       6 des,org,key,sv
                                              0 -              0 -         speci
al                      EMBL flatfiles, all fields indexed
qanxflatexc       Nucleotide,Nucfeatures,Refseq OK  OK  OK  emboss    1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      EMBL flatfiles, no rodent file
qanxflatinc       Nucleotide,Nucfeatures        OK  OK  OK  emboss    1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      EMBL flatfiles, only rodent file
qanxgcg           Nucleotide,Nucfeatures        OK  OK  OK  embossgcg 1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      GCG format EMBL
qanxgcgall        Nucleotide,Nucfeatures        OK  OK  OK  embossgcg 1_all
                       6 sv,des,org,key
                                              0 -              0 -         speci
al                      GCG format EMBL indexed by dbxgcg with query fields
qanxgcgexc        Nucleotide,Nucfeatures        OK  OK  OK  embossgcg 1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      GCG format EMBL without prokaryotes
qanxgcginc        Nucleotide,Nucfeatures        OK  OK  OK  embossgcg 1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      GCG format EMBL only prokaryotes
qawfasta          Nucleotide                    OK  OK  OK  emblcd    6239_caeno
rhabditis_elegans      2 id,acc
                                              0 -              0 -         speci
al                      FASTA file wormpep entries
qawxfasta         Nucleotide                    OK  OK  OK  emboss    6239_caeno
rhabditis_elegans      2 id,acc
                                              0 -              0 -         speci
al                      FASTA file wormpep entries
qaxembl           Nucleotide,Nucfeatures,Refseq OK  OK  OK  emboss    1_all
                       2 id,acc
                                              0 -              0 -         speci
al                      EMBL flatfiles
tembl             Nucleotide,Refseq,Nucfeatures OK  OK  OK  emblcd    1_all
                       6 sv,des,org,key
                                              0 -              1 x13776    speci
al  57                  EMBL in native format with EMBL CD-ROM index
temblall          Nucleotide,Nucfeatures,Refseq OK  OK  OK  direct    1_all
                       6 sv,des,org,key
                                              0 -              0 -         speci
al  57                  EMBL in native format with EMBL CD-ROM index
temblrest         Nucleotide,Nucfeatures,Refseq OK  OK  OK  direct    1_all
                       6 sv,des,org,key
                                              0 -              0 -         speci
al  57                  EMBL in native format with EMBL CD-ROM index
temblvrt          Nucleotide,Nucfeatures        OK  OK  OK  direct    9711_chord
ata                    6 sv,des,org,key
                                              0 -              0 -         speci
al  57                  EMBL in native format with EMBL CD-ROM index
tensembldasgrch37 Nucleotide                    OK  OK  -   das       9606_homo_
sapiens                2 id,acc
                                              0 -              0 -         speci
al                      Homo_sapiens Reference server based on GRCh37 assembly
testdb            Nucleotide                    OK  OK  OK  emblcd    -
                       3 des
                                              0 -              0 -         speci
al  01                  test sequence data
tgb               Nucleotide,Nucfeatures        OK  OK  OK  srswww    1_all
                       6 sv,des,org,key
                                              0 -              0 -         speci
al                      Genbank by SRS at DKFZ
tgenbank          Nucleotide,Nucfeatures        OK  OK  OK  emblcd    1_all
                       6 sv,des,org,key
                                              0 -              0 -         speci
al  01                  Test GenBank in native format with EMBL CD-ROM index
tgenedashuman     Nucleotide                    OK  OK  -   das       9606_homo_
sapiens                2 id,acc
                                              0 -              0 -         speci
al                      The Ensembl human Gene_ID reference source
tflybase          Features                      OK  -   -   chado(id) 1_all
                       2 uniquename
                                              0 -              0 -         speci
al                      Flybase CHADO server
tgenedb           Features                      OK  -   -   chado(id) 1_all
                       2 uniquename
                                              0 -              0 -         speci
al                      GeneDb CHADO server
ttax              Taxonomy                      OK  OK  OK  embosstax -
                       7 id,acc,nam,rnk,up,gc,mgc
                                              0 -              0 -         speci
al                      NCBI taxonomy test data
taxon             Taxonomy                      OK  OK  OK  embosstax 1
                       7 id,acc,tax,rnk,up,gc,mgc
                                              0 -              0 -         stand
ard July 2012           NCBI taxonomy
drcat             Resource                      OK  OK  OK  emboss    none
                      21 id,acc,nam,des,url,cat,edat,efmt,eid,etpc,xref,qout,qfm
t,qin,qurl,cc,rest,soap,stat,xref,taxid       0 -              0 -         stand
ard alpha 1 21-jun-2011 Data Resource Catalogue
tedam             Obo                           OK  OK  OK  emboss    -
                      12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,i
ssrc                                          0 -              0 -         speci
al  beta11              Test EDAM using dbxedam test indexes
tobo              Obo                           OK  OK  OK  emboss    -
                      12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,i
ssrc                                          0 -              0 -         speci
al  beta11              Test EDAM using dbxobo test indexes
chebi             Obo                           OK  OK  OK  emboss    none
                       5 id,acc,nam,isa,des
                                              0 -              0 -         stand
ard 93                  Chemical Entities of Biological Interest
eco               Obo                           OK  OK  OK  emboss    none
                       5 id,acc,nam,isa,des
                                              0 -              0 -         stand
ard 2.02                Evidence code ontology
edam              Obo                           OK  OK  OK  emboss    none
                      12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,i
ssrc                                          0 -              0 -         stand
ard 1.1                 EMBRACE Data and Methods ontology
edam_data         Obo                           OK  OK  OK  emboss    none
                      12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,i
ssrc                                          0 -              0 -         stand
ard 1.1                 EMBRACE Data and Methods ontology (data)
edam_format       Obo                           OK  OK  OK  emboss    none
                      12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,i
ssrc                                          0 -              0 -         stand
ard 1.1                 EMBRACE Data and Methods ontology (formats)
edam_identifier   Obo                           OK  OK  OK  emboss    none
                      12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,i
ssrc                                          0 -              0 -         stand
ard 1.1                 EMBRACE Data and Methods ontology (identifiers)
edam_operation    Obo                           OK  OK  OK  emboss    none
                      12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,i
ssrc                                          0 -              0 -         stand
ard 1.1                 EMBRACE Data and Methods ontology (operations)
edam_topic        Obo                           OK  OK  OK  emboss    none
                      12 id,acc,nam,isa,des,ns,hasattr,hasin,hasout,isid,isfmt,i
ssrc                                          0 -              0 -         stand
ard 1.1                 EMBRACE Data and Methods ontology (topics)
go                Obo                           OK  OK  OK  emboss    1_all
                       6 id,acc,nam,isa,des,ns
                                              0 -              0 -         stand
ard 1.1.3300            Gene Ontology
go_component      Obo                           OK  OK  OK  emboss    1_all
                       6 id,acc,nam,isa,des,ns
                                              0 -              0 -         stand
ard 1.1.3300            Gene Ontology (cellular components)
go_function       Obo                           OK  OK  OK  emboss    1_all
                       6 id,acc,nam,isa,des,ns
                                              0 -              0 -         stand
ard 1.1.3300            Gene Ontology (molecular functions)
go_process        Obo                           OK  OK  OK  emboss    1_all
                       6 id,acc,nam,isa,des,ns
                                              0 -              0 -         stand
ard 1.1.3300            Gene Ontology (biological processes)
pw                Obo                           OK  OK  OK  emboss    1_all
                       5 id,acc,nam,isa,des
                                              0 -              0 -         stand
ard 12:06:2012 11:03    Pathways ontology
ro                Obo                           OK  OK  OK  emboss    none
                       5 id,acc,nam,isa,des
                                              0 -              0 -         stand
ard 20:03:2009 11:58    Relations ontology
so                Obo                           OK  OK  OK  emboss    none
                       5 id,acc,nam,isa,des
                                              0 -              0 -         stand
ard 02:05:2012 11:08    Sequence ontology
swo               Obo                           OK  OK  OK  emboss    none
                       5 id,acc,nam,isa,des
                                              0 -              0 -         stand
ard 12-jul-2012         Software ontology

Command line arguments

Display information on configured databases
Version: EMBOSS:6.6.0.0

   Standard (Mandatory) qualifiers: (none)
   Additional (Optional) qualifiers:
   -database           string     Name of a single database to give
                                  information on (Any string)
   -html               boolean    [N] Format output as an HTML table
   -[no]protein        boolean    [Y] Display protein databases
   -[no]nucleic        boolean    [Y] Display nucleotide databases
   -[no]sequence       boolean    [Y] Display general sequence databases
   -[no]feature        boolean    [Y] Display feature annotation databases
   -[no]text           boolean    [Y] Display text databases
   -[no]taxonomy       boolean    [Y] Display taxonomy databases
   -[no]resource       boolean    [Y] Display resource databases
   -[no]assembly       boolean    [Y] Display sequence assembly databases
   -[no]obo            boolean    [Y] Display obo bio-ontology databases
   -[no]xml            boolean    [Y] Display XML databases
   -[no]standard       boolean    [Y] Display standard databases
   -[no]user           boolean    [Y] Display user-defined databases
   -[no]include        boolean    [Y] Display databases defined in included
                                  files
   -full               boolean    [N] Display all columns
   -access             boolean    [$(full)] This displays the levels of access
                                  that can be used on this database
   -methods            boolean    [$(full)] This displays the access methods
                                  that can be used on this database, for all,
                                  query or ID access
   -taxscope           boolean    [$(full)] This displays the taxons covered
                                  by this database
   -fields             boolean    [$(full)] This displays the search fields
                                  that can be used on this database, including
                                  the standard 'id' or 'acc' fields
   -numfields          boolean    [$(full)] This displays the number of search
                                  fields that can be used on this database,
                                  including the standard 'id' or 'acc' fields
   -aliases            boolean    [$(full)] This displays the alias names that
                                  can be used for this database
   -numaliases         boolean    [$(full)] This displays the number of alias
                                  names that can be used for this database
   -examples           boolean    [$(full)] This displays the example queries
                                  that can be used to test this database
   -numexamples        boolean    [$(full)] This displays the number of
                                  example queries that can be used to test
                                  this database
   -defined            boolean    [$(full)] This displays a short name for the
                                  file containing the database definition
   -release            boolean    [$(full)] Display 'release' column
   -outfile            outfile    [stdout] Output file name

   Advanced (Unprompted) qualifiers:
   -only               toggle     [N] This is a way of shortening the command
                                  line if you only want a few standard columns
                                  to be displayed. Instead of specifying:
                                  '-nohead -notype -noid -noquery -noall'
                                  to get only the comment output, you can
                                  specify
                                  '-only -comment'
   -heading            boolean    [@(!$(only))] Display column headings
   -type               boolean    [@(!$(only))] Display 'type' column
   -id                 boolean    [@(!$(only))] Display 'id' access column
   -query              boolean    [@(!$(only))] Display 'qry' access column
   -all                boolean    [@(!$(only))] Display 'all' access column
   -comment            boolean    [@(!$(only))] Display 'comment' column

   Associated qualifiers:

   "-outfile" associated qualifiers
   -odirectory         string     Output directory

   General qualifiers:
   -auto               boolean    Turn off prompts
   -stdout             boolean    Write first file to standard output
   -filter             boolean    Read first file from standard input, write
                                  first file to standard output
   -options            boolean    Prompt for standard and additional values
   -debug              boolean    Write debug output to program.dbg
   -verbose            boolean    Report some/full command line options
   -help               boolean    Report command line options and exit. More
                                  information on associated and general
                                  qualifiers can be found with -help -verbose
   -warning            boolean    Report warnings
   -error              boolean    Report errors
   -fatal              boolean    Report fatal errors
   -die                boolean    Report dying program messages
   -version            boolean    Report version number and exit

Input file format

   showdb examines the databases defined for this EMBOSS installation and
   for the current user.

  Input files for usage example 3

   'tsw' is a sequence entry in the example protein database 'tsw'

Output file format

  Output files for usage example 2

  File: showdb.out

# Name            Type                          Comment
# =============== ============================= =======
bpsw              Protein,Protfeatures          BioPerl OBDA index of test Swiss
Prot
bpworm            Protein                       BioPerl OBDA index of test wormp
ep fasta file
qapblast          Protein                       BLAST swissnew
qapblastall       Protein                       BLAST swissnew, all fields index
ed
qapblastsplit     Protein                       BLAST swissnew split in 5 files
qapblastsplitexc  Protein                       BLAST swissnew split in 5 files,
 not file 02
qapblastsplitinc  Protein                       BLAST swissnew split in 5 files,
 only file 02
qapfasta          Protein                       FASTA file swissnew entries
qapflat           Protein,Protfeatures          SpTrEmbl flatfile
qapflatall        Protein,Protfeatures          SpTrEmbl flatfiles, all fields i
ndexed
qapir             Protein,Protfeatures          Test PIR indexed by dbigcg
qapirall          Protein,Protfeatures          Test PIR indexed by dbigcg with
fields
qapirexc          Protein,Protfeatures          Test PIR indexed by dbigcg excep
t file pir1
qapirinc          Protein,Protfeatures          Test PIR indexed by dbigcg file
pir1
qapxfasta         Protein                       FASTA file swissnew entries
qapxflat          Protein                       Swissnew flatfiles
qasrswww          Protein,Protfeatures          Remote SRS web server
qaxpir            Protein,Protfeatures          PIR indexed by dbxgcg
qaxpirall         Protein,Protfeatures          Test PIR indexed by dbxgcg with
fields
qaxpirexc         Protein,Protfeatures          Test PIR indexed by dbxgcg excep
t pir1
qaxpirinc         Protein,Protfeatures          Test PIR indexed by dbxgcg file
pir1
tpir              Protein                       Test PIR using NBRF access for 4
 files
tsw               Protein,Protfeatures,Text     Swissprot native format with EMB
L CD-ROM index
tswnew            Protein,Protfeatures          SpTrEmbl as 3 files in native fo
rmat with EMBL CD-ROM index
bpembl            Nucleotide,Nucfeatures        BioPerl OBDA index of test EMBL
bpgb              Nucleotide,Nucfeatures        BioPerl OBDA index of test GenBa
nk
ena               Nucleotide,Nucfeatures        ENA via URL
qanfasta          Nucleotide                    FASTA file EMBL rodents
qanfastaall       Nucleotide                    FASTA file EMBL rodents, all fie
lds indexed
qanflat           Nucleotide,Nucfeatures,Refseq EMBL flatfiles
qanflatall        Nucleotide,Nucfeatures,Refseq EMBL flatfiles
qanflatexc        Nucleotide,Nucfeatures        EMBL flatfiles, no rodent file
qanflatinc        Nucleotide,Nucfeatures        EMBL flatfiles, only rodent file
qangcg            Nucleotide,Nucfeatures        GCG format test EMBL
qangcgall         Nucleotide,Nucfeatures        GCG format test EMBL
qangcgexc         Nucleotide,Nucfeatures        GCG format test EMBL without pro
karyotes
qangcginc         Nucleotide,Nucfeatures        GCG format test EMBL only prokar
yotes
qanxfasta         Nucleotide                    FASTA file EMBL rodents
qanxfastaall      Nucleotide                    FASTA file EMBL rodents, all fie
lds indexed
qanxflat          Nucleotide,Nucfeatures,Refseq EMBL flatfiles
qanxflatall       Nucleotide,Nucfeatures,Refseq EMBL flatfiles, all fields index
ed
qanxflatexc       Nucleotide,Nucfeatures,Refseq EMBL flatfiles, no rodent file
qanxflatinc       Nucleotide,Nucfeatures        EMBL flatfiles, only rodent file
qanxgcg           Nucleotide,Nucfeatures        GCG format EMBL
qanxgcgall        Nucleotide,Nucfeatures        GCG format EMBL indexed by dbxgc
g with query fields
qanxgcgexc        Nucleotide,Nucfeatures        GCG format EMBL without prokaryo
tes
qanxgcginc        Nucleotide,Nucfeatures        GCG format EMBL only prokaryotes
qawfasta          Nucleotide                    FASTA file wormpep entries
qawxfasta         Nucleotide                    FASTA file wormpep entries
qaxembl           Nucleotide,Nucfeatures,Refseq EMBL flatfiles
tembl             Nucleotide,Refseq,Nucfeatures EMBL in native format with EMBL
CD-ROM index
temblall          Nucleotide,Nucfeatures,Refseq EMBL in native format with EMBL
CD-ROM index
temblrest         Nucleotide,Nucfeatures,Refseq EMBL in native format with EMBL
CD-ROM index
temblvrt          Nucleotide,Nucfeatures        EMBL in native format with EMBL
CD-ROM index
tensembldasgrch37 Nucleotide                    Homo_sapiens Reference server ba
sed on GRCh37 assembly
testdb            Nucleotide                    test sequence data
tgb               Nucleotide,Nucfeatures        Genbank by SRS at DKFZ
tgenbank          Nucleotide,Nucfeatures        Test GenBank in native format wi
th EMBL CD-ROM index
tgenedashuman     Nucleotide                    The Ensembl human Gene_ID refere
nce source
tflybase          Features                      Flybase CHADO server
tgenedb           Features                      GeneDb CHADO server
ttax              Taxonomy                      NCBI taxonomy test data
taxon             Taxonomy                      NCBI taxonomy
drcat             Resource                      Data Resource Catalogue
tedam             Obo                           Test EDAM using dbxedam test ind
exes
tobo              Obo                           Test EDAM using dbxobo test inde
xes
chebi             Obo                           Chemical Entities of Biological
Interest
eco               Obo                           Evidence code ontology
edam              Obo                           EMBRACE Data and Methods ontolog
y
edam_data         Obo                           EMBRACE Data and Methods ontolog
y (data)
edam_format       Obo                           EMBRACE Data and Methods ontolog
y (formats)
edam_identifier   Obo                           EMBRACE Data and Methods ontolog
y (identifiers)
edam_operation    Obo                           EMBRACE Data and Methods ontolog
y (operations)
edam_topic        Obo                           EMBRACE Data and Methods ontolog
y (topics)
go                Obo                           Gene Ontology
go_component      Obo                           Gene Ontology (cellular componen
ts)
go_function       Obo                           Gene Ontology (molecular functio
ns)
go_process        Obo                           Gene Ontology (biological proces
ses)
pw                Obo                           Pathways ontology
ro                Obo                           Relations ontology
so                Obo                           Sequence ontology
swo               Obo                           Software ontology

   The output is a simple text table.

   Type 'P' indicates that this is a Protein database.

   Type 'N' indicates that this is a Nucleic database.

   'OK' under ID, Qry or All indicates that that access method can be used
   on this database. A '-' indicates that you cannot access this database
   in that way.

   Note that 'OK' does not mean that the database is working correctly. It
   simply means that showdb has read the database definition correctly and
   that this method of access to the database should be possible.

   If you are setting up a new database, then you should check that it
   works correctly by extracting entries from it using seqret.

   When the -html qualifier is specified, then the output will be wrapped
   in HTML tags, ready for inclusion in a Web page. Note that tags such as
   , ,  and  are not output by this program as
   the table of databases is expected to form only part of the contents of
   a web page - the rest of the web page must be supplied by the user.

Data files

   The databases are specified in the files "emboss.defaults" for site
   wide definitions, and "~/.embossrc" for the user's own settings.

Notes

   EMBOSS provides excellent database support. All the common sequence
   formats you are likely to come across are supported. There are three
   basic levels of database query with different ways to search for and
   retrieve entries: entry A single entry specified by database ID or
   accession number is retrieved. For example "embl:x13776". query One or
   more entries matching a wildcard string in the USA are retrieved (this
   can be slow for some methods). For example you can specify all of the
   human PAX proteins in SWISS_PROT by: swissprot:pax*_human. all All
   entries are read sequentially from a database. For example to specify
   all entries in the database use embl:*.

   One or more query levels may be available for a database depending on
   the database in question and how it has been setup and indexed. Each
   database and access method must be configured for it to be available
   for use. This involves editing one of the EMBOSS configuration files,
   either your own personal .embossrc or the installation-wide
   emboss.default file. The emboss.default file will typically contain the
   definitions of the test databases (tsw, tembl, tpir, etc) used in the
   usage examples for the application documentation and serve as example
   database definitions. For more information, see the EMBOSS
   Administrators Manual. You can run showdb to see the databases and
   access methods that have been configured successfully.

References

   None.

Warnings

   Where the string OK is given next to a database is listed in showdb
   output, this means showdb has read the database definition correctly
   and that this access method is in principle possible, in other words,
   the database has been configured correctly.. It does not mean that the
   database or access method are available or working correctly. You
   should check things are ok by running, for example, seqret to retrieve
   an entry.

Diagnostic Error Messages

   "The database 'xyz' does not exist" You have supplied the name of a
   database with the -database qualifier, but that database does not exist
   as far as EMBOSS is concerned.

Exit status

   It always exits with status 0, unless the above diagnostic message is
   displayed.

Known bugs

   None noted.

See also

   Program name     Description
   cachedas         Generate server cache file for DAS servers or for the DAS
                    registry
   cachedbfetch     Generate server cache file for Dbfetch/WSDbfetch data
                    sources
   cacheebeyesearch Generate server cache file for EB-eye search domains
   cacheensembl     Generate server cache file for an Ensembl server
   dbtell           Display information about a public database
   servertell       Display information about a public server
   showserver       Display information on configured servers

Author(s)

   Gary Williams formerly at:
   MRC Rosalind Franklin Centre for Genomics Research Wellcome Trust
   Genome Campus, Hinxton, Cambridge, CB10 1SB, UK

   Please report all bugs to the EMBOSS bug team
   (emboss-bug (c) emboss.open-bio.org) not to the original author.

History

   Completed 6th August 1999.

Target users

   This program is intended to be used by everyone and everything, from
   naive users to embedded scripts.

Comments

   None
