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How can I use python for transforming gene information

Hi!

I was given a list of human genes (about a 1,000) on which I need to perform the next assignments:

  1. Look up the gene's sequences on geneCards (or some other server).

  2. Take their sequences and first separate them into domainswith Pfam (http://pfam.xfam.org/search), Motifs (http://myhits.isb-sib.ch/cgi-bin/motif_scan).

Can someone please give me general directions on how or where to start from?

Thanks!

genome gene sequence sequencing
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written by shakedtt • shakedtt

A good place to start would be the Biopython Cookbook and tutorial. The first part, getting the sequences, should be obvious if you check the Cookbook.

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written by WouterDeCoster WouterDeCoster

1 answer

I would say, open a text editor and start writing...

This looks like a homework assignment to me, you'll never learn it by letting some-one else do it for you.

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written by Benn Benn

Nope - just helping a friend that works in a lab....

I'm asking for help because I've never tried to write a python's code that interact with web servers :/

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written by shakedtt • shakedtt

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