[Bioperl-l] Genbank parser

Jason Stajich jason.stajich at duke.edu
Tue Nov 1 17:47:50 EST 2005

Bio::SeqIO parses genbank files.
There is a spliced_seq method to splice CDS sequence out from a set of

See the HOWTOs for sequence introduction and feature and annotation  

and particularly the tutorial as well:


On Oct 30, 2005, at 8:35 PM, Bingshan Li wrote:

> Hi All,
> I am new to Bioperl and recently found it has a lot of useful  
> modules. I wrote a perl script to extract all protein sequences and  
> corresponding coding sequences from Genbank files. But I found some  
> bugs and it's hard to make sue my script is bug free after several  
> revision. I am wondering if there are some modules and specific  
> functions to use to fulfill my requirement. Does anybody have  
> similar code to share with? Most bugs come from multiple segments  
> of coding sequences and some cds sequences are on the minus strand.
> Thanks a lot!
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Jason Stajich
Duke University

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