Bioperl: module for sequence content analysis?
Gatherer, D. (Derek)
Mon, 17 Jan 2000 09:14:21 +0100
>> Is there a Bioperl module that has a method returning the codon frequency
>> table, or amino acid frequency table, or some other kind of hashed
>> data for Bio::Seq objects? I am most interested in overlapping triplet
>> frequencies in large FASTA-formatted databases.
>Not that I know of. If you write something, please contribute...
Yes, I hope I can. Reading the Seq.pm POD over the weekend made me wonder
if perhaps the best way of doing it might be to add a method to Seq.pm...???
The translate function already does quite a lot of the spade work in terms
of checking the alphabet, and then setting up the loop over the sequence.
It might just be a matter of modifying the loop so that it slides ++ instead
of jumping +=3, and then racking up the triplets in a hash instead of
changing them to amino acids.
Is there perhaps a more parsimonious way of doing it? If there is, I
haven't spotted it. Except perhaps... I was thinking of doing this as a
different but similar function to translate, whereas it may be that they
share enough code to make it an option _within_ translate??? This is
perhaps quite sneaky, but I haven't thought it through properly.
Also, should this thread transfer to perl-guts?
Organon Laboratories Ltd
Scotland ML1 5SH
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