[Bioperl-l] new bioperl script

Carnë Draug carandraug+dev at gmail.com
Mon Jul 18 01:57:33 UTC 2011


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

Carnë Draug

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