[Bioperl-l] Re: asking for a help

Jason Stajich jason at cgt.duhs.duke.edu
Thu Mar 25 08:03:33 EST 2004

Joshua -

You can translate sequence within bioperl directly (if they are spliced
and you know their frame) with the method $seq->translate().  If they are
annotations in genbank/embl format you can use the $feature->splice_seq to
get the spliced exons out of the sequence, but you will probably have to
read more about the Sequences and Features before this will make sense.

You should read the bioperl Feature and Sequence HOWTO first linked off
the HOWTO page on the bioperl website.

Bio::Factory and Bio::Tools::Run modules are in bioperl-run package which
is available from the bioperl distribution directory

On Wed, 24 Mar 2004 szhan at uoguelph.ca wrote:

> Hello, Jason:
> I have got a list of genes (nucleotides sequences), I want to translate them
> using a program (transeq) in EMBOSS and compare their function similarity
> using blastp of bl2seq in BLAST. I read FAQ in bioperl web site and it said
> that I can find a module: Bio::Factory::EMBOSS to do that, but I could not
> find it. Could you please give me a guide to do this job?
> Your help will be highly appreciated!
> Joshua

Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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