Common running modes

Running modes for genewise (genomic to protein comparisons).

NB, the order of the -options are not important, but the protein file must be before the dna file

• genewise protein.pep cosmid.dna compares a protein sequence to a DNA sequence (same as the example above)
• genewise -hmmer pkinase.hmm cosmid.dna compares a protein profile HMM to a DNA sequence
• genewisedb protein.pep human.fa compares a single protein sequence to a database of DNA sequences
• genewisedb -hmmer pkinase.hmm human.fa compares a single protein profile HMM to a database of DNA sequences
• genewisedb -prodb protein.pep -dnas cosmid.dna compares a database of protein sequences to a single dna sequence
• genewisedb -pfam Pfam -dnas cosmid.dna compares a database of protein profile HMMs to a single dna sequence
• genewisedb -prodb protein.pep human.fa compares a database of protein sequences to a database dna sequences - beware, this will take a while!
• genewisedb -pfam Pfam human.fa compares a database of protein profile HMMs to a database of single sequences - beware, this will take a while

The estwise (protein to est/cDNA comparisons) have precisely the same running modes. Listed for completeness below

• estwise protein.pep singleest.fa compares a protein sequence to a DNA sequence (same as the example above)
• estwise -hmmer pkinase.hmm singleest.fa compares a protein profile HMM to a DNA sequence
• estwisedb protein.pep est.fa compares a single protein sequence to a database of DNA sequences
• estwisedb -hmmer pkinase.hmm est.fa compares a single protein profile HMM to a database of DNA sequences
• estwisedb -prodb protein.pep -dnas singleest.fa compares a database of protein sequences to a single dna sequence
• estwisedb -pfam Pfam -dnas singleest.fa compares a database of protein profile HMMs to a single dna sequence
• estwisedb -prodb protein.pep est.fa compares a database of protein sequences to a database dna sequences - beware, this will take a while!
• estwisedb -pfam Pfam est.fa compares a database of protein profile HMMs to a database of single sequences - beware, this will take a while