HOWTO Discussion:Beginners

Can we add links for the method names to the entries in doc.bioperl.org? This would make it easier to look to methods on object directly from the how-to. --Golharam

shouldn't

@params = (-program  => 'blastn', -database => 'db.fa');

be

@params = (program  => 'blastn', database => 'db.fa');

At least the first doesn't work for me while the latter does.

• Added this in. Thanks! --Chris Fields 11:27, 9 May 2007 (EDT)

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I found that the following links are broken: Object Oriented Perl The ENSEMBL Perl API

And this one is missing a link: The Bioperl design documentation --Slowkow 03:40, 16 March 2010 (UTC)

• Found and fixed. Thanks! --Dave Messina 10:11, 16 March 2010 (UTC)

I am a beginner in BioPerl but in the example illustrating the use of the Bio::DB::Fasta module, I think that the piece of code

$seqobj = $db->get_Seq_by_id($id,$start,$end);
print $seqobj->seq

should be replaced with

$seqobj = $db->get_Seq_by_id($id);
print $seqobj->subseq($start,$end);

because the get_Seq_by_id method only accepts one (the ID) argument. In my hands at least, the first doesn't work (the whole sequence is returned) while the latter does. --Lasserre 09:00, 23 July 2010 (UTC)