[Bioperl-l] Bio::DB::CUTG problem

Csaba Ortutay csaba.ortutay at uta.fi
Thu Mar 4 04:57:00 EST 2010


We would use Bio::DB::CUTG module to get codon usage data for a large number 
of genomes.

We have noticed that the module cannot findcertain organisms which are 
otherwise in the database. It happens when the name contains some non-
alphabetic characters.

A few examples:

Streptococcus agalactiae 2603V/R
Shigella flexneri 5 str. 8401

I have located the corresponding part in the CUTG.pm code, and I would suggest 
a change:

<       my $nameparts =  join "+", $self->sp =~ /(\w+)/g;
>       my $nameparts =  join "+", $self->sp =~ /(\S+)/g;

With this I can now access the wanted tables.

Best regards,

Csaba Ortutay PhD
Docent of Bioinformatics
IMT Bioinformatics
University of Tampere

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