Wise2 - database searching mode
Program: genewisedb version: $Name: wise2-4-1 $ released: unreleased
This program is freely distributed under a GNU General Public License.
   See -version for more info on copyright
Bugs and credits to Ewan Birney <birney@sanger.ac.uk>
-----------------------------------------------------

Algorithm type:        GeneWise
Search algorithm used: 623
Implementation:        Single Threaded processor (serial)
Search mode:           Single protein vs genomic db
Protein info from:     rrm.HMM
Dna info from:         dna.db
Start/End (protein)    global
Gene Paras:            /usr/share/wise/human.gf
Codon Table:           /usr/share/wise/codon.table
Subs error:            1e-05
Indel error:           1e-05
Model splice?          model
Model codon bias?      flat
Model intron bias?     tied
Null model             syn
Alignment Alg          623L
[Warning: Can't fit histogram to a db smaller than 1,000]


#
#WARNING!
#
# Your alignment algorithm is different from your search algorithm.
# This is probably quite sensible but will lead to differing scores.
# Use the search score as an indicator of the significance of the match
# Read the docs for more information
#


#High Score list
#Protein ID                 DNA Str  ID                        Bits Evalue
--------------------------------------------------------------------------
Protein SEED                DNA [+] MMD728                   101.74
Protein SEED                DNA [+] MMD729                   101.74
Protein SEED                DNA [+] MMFLI2X                  101.74
Protein SEED                DNA [+] SAHNRNPH                 86.11


#Alignments
-----------------------------------------------------------------------

>Results for SEED vs MMD728 (forward) [0]

genewisedb output
Score 179.66 bits over entire alignment.
This will be different from per-alignment scores. See manual for details
For computer parsable output, try genewisedb -help or read the manual
Scores as bits over a synchronous coding model

                                                                       
                                                                       
                                                                       
                                                                       
                                                                       
                     Alignment 1 Score 86.15 (Bits)                    


SEED               1 LFVGNLPPDVTEEDLKDLFSKFGPIVSIKIVRDIIEKPKETGKSKGFAF 
                     LF+G+L++++T+E L+ +F++ G  +++ ++RD     ++T++S+GF+F 
                     LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRD-----PNTKRSRGFGF 
MMD728            70 ctaggcatgaaggacaactgctgacagtggaag     caaaatagtgt 
                     tttggtgtaccaagtggataaggctcagtttga     cacagcggtgt 
                     cccaggccaaccgtggcttgagaaaactgagat     accgacgctgt 


SEED              50 VEFESEEDAEKALEALNGKELGGRKLRV                      
                     V+++++E++++A++    ++++GR+++                       
                     VTYATVEEVDAAMN-ARPHKVDGRVVEP                      
MMD728           202 gatgagggggggaa gaccagggagggc                      
                     tcacctaataccta cgcaataggttac                      
                     catctgaagttcgt aaacggtaatgat                      


                                                                       
                                                                       
                                                                       
                                                                       
                                                                       
                     Alignment 2 Score 93.51 (Bits)                    


SEED               1 LFVGNLPPDVTEEDLKDLFSKFGPIVSIKIVRDIIEKPKETGKSKGFAF 
                      FVG++ +D+ E+ L+D+F+++G+I+ I+I++D     +  GK +GFAF 
                     IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD-----RGSGKKRGFAF 
MMD728           343 atgggaaggaggccccgttgctgaaggagaaag     agagaaagtgt 
                     tttggtaaacaaaatgaataaagatattattca     ggggaaggtct 
                     ctttttaactaatcaatttggtggtagaatgtc     actgaggcttt 


SEED              50 VEFESEEDAEKALEALNGKELGGRKLRV                      
                     V+F+++++++K +     ++++G++++V                      
                     VTFDDHDSVDKIVI-QKYHTVNGHNCEV                      
MMD728           475 gatggcgtggaaga catcagagcatgg                      
                     tctaaaactaattt aaaactagaagat                      
                     tcttctctgtgttt gacttgtccctaa                      


//
Gene 1
Gene 70 282 
  Exon 70 282 phase 0
Gene 2
Gene 343 555 
  Exon 343 555 phase 0
//
>MMD728.[70:282].sp.tr
LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR
PHKVDGRVVEP
>MMD728.[343:555].sp.tr
IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK
YHTVNGHNCEV
//
>MMD728.[70:282].sp
CTCTTCATCGGAGGGCTGAGCTTCGAAACAACCGACGAGAGTCTGAGGAGCCATTTTGAG
CAATGGGGAACACTAACAGACTGTGTGGTAATGAGAGATCCAAACACCAAGAGATCCAGG
GGCTTTGGGTTTGTCACATATGCCACTGTGGAAGAAGTGGATGCTGCCATGAATGCAAGA
CCACACAAGGTGGATGGAAGAGTTGTGGAACCT
>MMD728.[343:555].sp
ATCTTTGTTGGTGGTATTAAAGAAGACACTGAAGAACATCACCTACGAGATTATTTTGAG
CAGTATGGGAAGATTGAAGTGATAGAAATTATGACTGACAGAGGCAGTGGGAAAAAGAGG
GGCTTTGCTTTTGTTACCTTTGATGACCATGACTCTGTGGATAAGATTGTTATTCAGAAA
TACCATACTGTGAATGGCCACAACTGTGAAGTA
//
Sequence MMD728
subsequence MMD728.1 70 282

Sequence MMD728.1
CDS
Start_not_found
End_not_found
CDS_predicted_by genewise 86.15
source_Exons 1 213

Sequence MMD728
subsequence MMD728.2 343 555

Sequence MMD728.2
CDS
Start_not_found
End_not_found
CDS_predicted_by genewise 93.51
source_Exons 1 213

//
Gene 0
Gene 69 - 282
Transcript 0
Exon 0-213
Translation 0 - 213

Gene 1
Gene 342 - 555
Transcript 0
Exon 0-213
Translation 0 - 213

//

>Results for SEED vs MMD729 (forward) [1]

genewisedb output
Score 179.66 bits over entire alignment.
This will be different from per-alignment scores. See manual for details
For computer parsable output, try genewisedb -help or read the manual
Scores as bits over a synchronous coding model

                                                                       
                                                                       
                                                                       
                                                                       
                                                                       
                     Alignment 1 Score 86.15 (Bits)                    


SEED               1 LFVGNLPPDVTEEDLKDLFSKFGPIVSIKIVRDIIEKPKETGKSKGFAF 
                     LF+G+L++++T+E L+ +F++ G  +++ ++RD     ++T++S+GF+F 
                     LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRD-----PNTKRSRGFGF 
MMD729            70 ctaggcatgaaggacaactgctgacagtggaag     caaaatagtgt 
                     tttggtgtaccaagtggataaggctcagtttga     cacagcggtgt 
                     cccaggccaaccgtggcttgagaaaactgagat     accgacgctgt 


SEED              50 VEFESEEDAEKALEALNGKELGGRKLRV                      
                     V+++++E++++A++    ++++GR+++                       
                     VTYATVEEVDAAMN-ARPHKVDGRVVEP                      
MMD729           202 gatgagggggggaa gaccagggagggc                      
                     tcacctaataccta cgcaataggttac                      
                     catctgaagttcgt aaacggtaatgat                      


                                                                       
                                                                       
                                                                       
                                                                       
                                                                       
                     Alignment 2 Score 93.51 (Bits)                    


SEED               1 LFVGNLPPDVTEEDLKDLFSKFGPIVSIKIVRDIIEKPKETGKSKGFAF 
                      FVG++ +D+ E+ L+D+F+++G+I+ I+I++D     +  GK +GFAF 
                     IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD-----RGSGKKRGFAF 
MMD729           343 atgggaaggaggccccgttgctgaaggagaaag     agagaaagtgt 
                     tttggtaaacaaaatgaataaagatattattca     ggggaaggtct 
                     ctttttaactaatcaatttggtggtagaatgtc     actgaggcttt 


SEED              50 VEFESEEDAEKALEALNGKELGGRKLRV                      
                     V+F+++++++K +     ++++G++++V                      
                     VTFDDHDSVDKIVI-QKYHTVNGHNCEV                      
MMD729           475 gatggcgtggaaga catcagagcatgg                      
                     tctaaaactaattt aaaactagaagat                      
                     tcttctctgtgttt gacttgtccctaa                      


//
Gene 1
Gene 70 282 
  Exon 70 282 phase 0
Gene 2
Gene 343 555 
  Exon 343 555 phase 0
//
>MMD729.[70:282].sp.tr
LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR
PHKVDGRVVEP
>MMD729.[343:555].sp.tr
IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK
YHTVNGHNCEV
//
>MMD729.[70:282].sp
CTCTTCATCGGAGGGCTGAGCTTCGAAACAACCGACGAGAGTCTGAGGAGCCATTTTGAG
CAATGGGGAACACTAACAGACTGTGTGGTAATGAGAGATCCAAACACCAAGAGATCCAGG
GGCTTTGGGTTTGTCACATATGCCACTGTGGAAGAAGTGGATGCTGCCATGAATGCAAGA
CCACACAAGGTGGATGGAAGAGTTGTGGAACCT
>MMD729.[343:555].sp
ATCTTTGTTGGTGGTATTAAAGAAGACACTGAAGAACATCACCTACGAGATTATTTTGAG
CAGTATGGGAAGATTGAAGTGATAGAAATTATGACTGACAGAGGCAGTGGGAAAAAGAGG
GGCTTTGCTTTTGTTACCTTTGATGACCATGACTCTGTGGATAAGATTGTTATTCAGAAA
TACCATACTGTGAATGGCCACAACTGTGAAGTA
//
Sequence MMD729
subsequence MMD729.1 70 282

Sequence MMD729.1
CDS
Start_not_found
End_not_found
CDS_predicted_by genewise 86.15
source_Exons 1 213

Sequence MMD729
subsequence MMD729.2 343 555

Sequence MMD729.2
CDS
Start_not_found
End_not_found
CDS_predicted_by genewise 93.51
source_Exons 1 213

//
Gene 0
Gene 69 - 282
Transcript 0
Exon 0-213
Translation 0 - 213

Gene 1
Gene 342 - 555
Transcript 0
Exon 0-213
Translation 0 - 213

//

>Results for SEED vs MMFLI2X (forward) [2]

genewisedb output
Score 179.66 bits over entire alignment.
This will be different from per-alignment scores. See manual for details
For computer parsable output, try genewisedb -help or read the manual
Scores as bits over a synchronous coding model

                                                                       
                                                                       
                                                                       
                                                                       
                                                                       
                     Alignment 1 Score 86.15 (Bits)                    


SEED               1 LFVGNLPPDVTEEDLKDLFSKFGPIVSIKIVRDIIEKPKETGKSKGFAF 
                     LF+G+L++++T+E L+ +F++ G  +++ ++RD     ++T++S+GF+F 
                     LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRD-----PNTKRSRGFGF 
MMFLI2X          105 ctaggcatgaaggacaactgctgacagtggaag     caaaatagtgt 
                     tttggtgtaccaagtggataaggctcagtttga     cacagcggtgt 
                     cccaggccaaccgtggcttgagaaaactgagat     accgacgctgt 


SEED              50 VEFESEEDAEKALEALNGKELGGRKLRV                      
                     V+++++E++++A++    ++++GR+++                       
                     VTYATVEEVDAAMN-ARPHKVDGRVVEP                      
MMFLI2X          237 gatgagggggggaa gaccagggagggc                      
                     tcacctaataccta cgcaataggttac                      
                     catctgaagttcgt aaacggtaatgat                      


                                                                       
                                                                       
                                                                       
                                                                       
                                                                       
                     Alignment 2 Score 93.51 (Bits)                    


SEED               1 LFVGNLPPDVTEEDLKDLFSKFGPIVSIKIVRDIIEKPKETGKSKGFAF 
                      FVG++ +D+ E+ L+D+F+++G+I+ I+I++D     +  GK +GFAF 
                     IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTD-----RGSGKKRGFAF 
MMFLI2X          378 atgggaaggaggccccgttgctgaaggagaaag     agagaaagtgt 
                     tttggtaaacaaaatgaataaagatattattca     ggggaaggtct 
                     ctttttaactaatcaatttggtggtagaatgtc     actgaggcttt 


SEED              50 VEFESEEDAEKALEALNGKELGGRKLRV                      
                     V+F+++++++K +     ++++G++++V                      
                     VTFDDHDSVDKIVI-QKYHTVNGHNCEV                      
MMFLI2X          510 gatggcgtggaaga catcagagcatgg                      
                     tctaaaactaattt aaaactagaagat                      
                     tcttctctgtgttt gacttgtccctaa                      


//
Gene 1
Gene 105 317 
  Exon 105 317 phase 0
Gene 2
Gene 378 590 
  Exon 378 590 phase 0
//
>MMFLI2X.[105:317].sp.tr
LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNAR
PHKVDGRVVEP
>MMFLI2X.[378:590].sp.tr
IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQK
YHTVNGHNCEV
//
>MMFLI2X.[105:317].sp
CTCTTCATCGGAGGGCTGAGCTTCGAAACAACCGACGAGAGTCTGAGGAGCCATTTTGAG
CAATGGGGAACACTAACAGACTGTGTGGTAATGAGAGATCCAAACACCAAGAGATCCAGG
GGCTTTGGGTTTGTCACATATGCCACTGTGGAAGAAGTGGATGCTGCCATGAATGCAAGA
CCACACAAGGTGGATGGAAGAGTTGTGGAACCT
>MMFLI2X.[378:590].sp
ATCTTTGTTGGTGGTATTAAAGAAGACACTGAAGAACATCACCTACGAGATTATTTTGAG
CAGTATGGGAAGATTGAAGTGATAGAAATTATGACTGACAGAGGCAGTGGGAAAAAGAGG
GGCTTTGCTTTTGTTACCTTTGATGACCATGACTCTGTGGATAAGATTGTTATTCAGAAA
TACCATACTGTGAATGGCCACAACTGTGAAGTA
//
Sequence MMFLI2X
subsequence MMFLI2X.1 105 317

Sequence MMFLI2X.1
CDS
Start_not_found
End_not_found
CDS_predicted_by genewise 86.15
source_Exons 1 213

Sequence MMFLI2X
subsequence MMFLI2X.2 378 590

Sequence MMFLI2X.2
CDS
Start_not_found
End_not_found
CDS_predicted_by genewise 93.51
source_Exons 1 213

//
Gene 0
Gene 104 - 317
Transcript 0
Exon 0-213
Translation 0 - 213

Gene 1
Gene 377 - 590
Transcript 0
Exon 0-213
Translation 0 - 213

//

>Results for SEED vs SAHNRNPH (forward) [3]

genewisedb output
Score 150.47 bits over entire alignment.
This will be different from per-alignment scores. See manual for details
For computer parsable output, try genewisedb -help or read the manual
Scores as bits over a synchronous coding model

                                                                       
                                                                       
                                                                       
                                                                       
                                                                       
                     Alignment 1 Score 77.89 (Bits)                    


SEED               1 LFVGNLPPDVTEEDLKDLFSKFGPIVSIKIVRDIIEKPKETGKSKGFAF 
                     LF+G+L + +T+E LK++F++ G+IV++ +++D     ++T++S+GF+F 
                     LFIGGLDYRTTDESLKQHFEQWGEIVDVVVMKD-----PKTKRSRGFGF 
SAHNRNPH         148 ctaggtgtaaaggtcacctgctggagggggaag     caaaatagtgt 
                     tttggtaagccaactaaataaggattattttaa     cacagcggtgt 
                     atttagctaatcgcagattaagtaattggtggc     taggggagtgc 


SEED              50 VEFESEEDAEKALEALNGKELGGRKLRV                      
                     +++     +++A +    ++++GR+++                       
                     ITYSRAHMVDDAQN-ARPHKVDGRVVEP                      
SAHNRNPH         280 aattagcaggggca gcccagggcgggc                      
                     tcacgcattaacaa cgcaataggttac                      
                     atccaatggtttgt tcacatttttggg                      


                                                                       
                                                                       
                                                                       
                                                                       
                                                                       
                     Alignment 2 Score 72.58 (Bits)                    


SEED               1 LFVGNLPPDVTEEDLKDLFSKFGPIVSIKIVRDIIEKPKETGKSKGFAF 
                     LFVG++ +++ E DL+D+F+++G +VS+ IV D     KET K +GFAF 
                     LFVGGIKEEMEENDLRDYFKQYGTVVSAAIVVD-----KETRKKRGFAF 
SAHNRNPH         421 ctgggaaggaggagccgttactgaggtggaggg     agacaacgtgt 
                     tttggtaaataaaatgaataaagcttcccttta     aacgaaggtct 
                     atttatgaggaactgcttcagtctccttacctc     ggtcggtcctc 


SEED              50 VEFESEEDAEKALEALNGKELGGRKLRV                      
                     VEF++ + ++K      +++++G+ + V                      
                     VEFDDYDPVDKICL-SRNHQIRGKHIDV                      
SAHNRNPH         553 ggtggtgcggaatt acaccacgacagg                      
                     tataaaactaatgt ggaaatggaatat                      
                     aatctttatcaatg tctcgctggtatc                      


//
Gene 1
Gene 148 360 
  Exon 148 360 phase 0
Gene 2
Gene 421 633 
  Exon 421 633 phase 0
//
>SAHNRNPH.[148:360].sp.tr
LFIGGLDYRTTDESLKQHFEQWGEIVDVVVMKDPKTKRSRGFGFITYSRAHMVDDAQNAR
PHKVDGRVVEP
>SAHNRNPH.[421:633].sp.tr
LFVGGIKEEMEENDLRDYFKQYGTVVSAAIVVDKETRKKRGFAFVEFDDYDPVDKICLSR
NHQIRGKHIDV
//
>SAHNRNPH.[148:360].sp
CTATTTATTGGTGGATTGGACTATAGAACAACTGACGAGTCCCTAAAGCAACATTTTGAA
CAATGGGGTGAAATAGTTGATGTGGTGGTTATGAAGGACCCTAAAACGAAGAGGTCGAGA
GGGTTTGGGTTCATAACTTACTCCAGAGCACATATGGTGGATGATGCTCAGAATGCTCGC
CCACACAAAGTTGATGGTCGTGTTGTGGAGCCG
>SAHNRNPH.[421:633].sp
CTATTTGTTGGTGGAATTAAGGAAGAGATGGAAGAAAACGATCTGCGCGATTATTTCAAA
CAGTATGGCACTGTCGTCTCTGCTGCAATCGTCGTTGACAAGGAGACTCGCAAGAAGCGT
GGCTTCGCTTTCGTAGAATTTGACGATTATGATCCAGTTGACAAAATATGTTTGAGTCGC
AATCACCAGATCCGTGGGAAGCATATAGATGTC
//
Sequence SAHNRNPH
subsequence SAHNRNPH.1 148 360

Sequence SAHNRNPH.1
CDS
Start_not_found
End_not_found
CDS_predicted_by genewise 77.89
source_Exons 1 213

Sequence SAHNRNPH
subsequence SAHNRNPH.2 421 633

Sequence SAHNRNPH.2
CDS
Start_not_found
End_not_found
CDS_predicted_by genewise 72.58
source_Exons 1 213

//
Gene 0
Gene 147 - 360
Transcript 0
Exon 0-213
Translation 0 - 213

Gene 1
Gene 420 - 633
Transcript 0
Exon 0-213
Translation 0 - 213

//
