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name promoterwise
desc promoterwise standard test
do   promoterwise -silent pw.human pw.mouse > TEMP-PW
diff TEMP-PW promoterwise.out
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name basic-cdna
desc cdna test case (protein v cdna), all outputs
do   estwise short.pep short.dna -indel 1e-5 -subs 1e-5 -pretty -para -sum -alb -pal -silent -alg 333 > TEMP
diff TEMP basic_cdna.out
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name basic-genomic
desc genomic test case (protein v genomic), all outputs
do   genewise short.pep short.dna -pretty -para  -genes -sum -cdna -trans -ace -gener -alb -pal -quiet -dymem linear  > TEMP
diff TEMP basic_genomic.out
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name hmm-binary-cdna
desc cdna test case (protein v cdna), all outputs
do   estwise HMM.binary -indel 1e-5 -subs 1e-5 -hmmer  short.dna -pretty -para -sum -alb -pal -quiet -alg 333L > TEMP
diff TEMP hmm_cdna.out
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name hmm-wrong-dna
desc HMMs vs DNA sequence when there is no match
do   genewise wrong.hmm -hmmer short.dna -alg 623 -pal > TEMP
diff TEMP wrong.out
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name hmm-wrong-dna-est
desc HMMs vs DNA sequence when there is no match
do   estwise wrong.hmm -hmmer short.dna -alg 333 -pal > TEMP
diff TEMP wrong_est.out
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name hmm-ascii-genomic
desc cdna test case (protein v cdna), all outputs
do   genewise -init local HMM.ascii -hmmer  short.dna -pretty -para  -genes -sum -cdna -trans -ace -gener -alb -pal -quiet > TEMP
diff TEMP hmm_genomic.out
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name genewise-db
desc genewisedb hmm vs DNA sequences. Could take a while
do   genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init global > TEMP
diff TEMP genewise-db.out
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name genewise-db-lite
desc genewisedb hmm vs DNA sequences, using GWLITE. Could take a while
do   genewisedb rrm.HMM -hmmer dna.db -pretty -para -gener -genes -cdna -trans -ace -quiet -init global -alg 6LITE > TEMP
diff TEMP genewise-db-lite.out
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name estwise-db
desc estwisedb hmm vs DNA sequences. Could take a while
do   estwisedb -init local rrm.HMM -hmmer dna.db -pretty -para -alb -quiet -alg 333 -aalg 333 > TEMP
diff TEMP estwise-db.out
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name pswdb
desc Protein smith waterman db search
do   pswdb road.pep pep.fa -quiet > TEMP 
diff TEMP pswdb.out
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name genewisedb-pfam-mode
desc genewisedb designed for Pfam searching
do   genewisedb -pfam rrm.HMM -dnas short.dna -pretty -para -alb -quiet -alg 623 -aalg 623L > TEMP
diff TEMP genewisedb-pfam.out
//
