[Bioperl-l] new bioperl script

[Jun Yin]

Hi, 
 
See this page for existing BioPerl modules retrieving sequences and annotations from NCBI database.
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook
 
Ensembl also has BioPerl like APIs for batch downloading sequences and annotations. So there is no need to implement it again.
http://www.ensembl.org/info/data/api.html
 
Cheers,
Jun

----- Original Message -----
From: Carnë Draug <carandraug+dev at gmail.com>
Date: Monday, July 18, 2011 4:26 am
Subject: [Bioperl-l] new bioperl script
To: bioperl-l at bioperl.org

> Hi
> 
> I've been working on a program to download sequences. I saw the
> scripts in bioperl and I thought it could be a good addition to them.
> The idea behind it is that given a list of queries, it searches the
> gene database and then downloads the gene sequence and it's associated
> products (only downloads the reference sequences although I may add
> support for alternates later).
> 
> There's options to have extra upstream or downstream base pairs, and
> the naming of the sequence files (such as using the gene name rather
> than the UID. Or use the UIDs or accessions of related sequences).
> It's still not completely finished. Currently it only searches on
> entrezgene database but I'll be extending it to Ensembl this week.
> 
> Would you be interested on something like this? I pasted it here
> http://pastebin.com/D3sY7hLb
> 
> Carnë Draug
> 
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