[Bioperl-l] Bio::Tools::TMHMM;

_Lelieveld, Stefan - s1012635 s1012635 at student.hsleiden.nl
Thu Sep 9 05:27:23 EDT 2010


Hi, 

I am a bio-informatics student working on a new project. For this project I need to get the TMHMM prediction of a list of proteins (in fasta format). 
I came across the Bio::Tools::TMHMM; package for BioPerl which looked promesing. The problem is I lack the advanced knowlegde of perl to get this package to work. So far we had courses in Python and Java not in Perl. 

http://search.cpan.org/~birney/bioperl-1.2.3/Bio/Tools/Tmhmm.pm : 
use Bio::Tools::Tmhmm; 
my $parser = new Bio::Tools::Tmhmm(-fh =>$filehandle ); 
while( my $tmhmm_feat = $parser->next_result ) { 
#do something 
#eg 
push @tmhmm_feat, $tmhmm_feat; 
} 

How do I feed a input.txt(containing the proteins as fasta format) to this parser and how do I save the output? 

cheers! 

Stefan Lelieveld 



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