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Bioperl Sequence Retrievalby DavyK (Initiate) |
on Sep 29, 2010 at 10:41 UTC ( [id://862582]=perlquestion: print w/replies, xml ) | Need Help?? |
DavyK has asked for the wisdom of the Perl Monks concerning the following question: Hi all, I am basically only starting to learn Perl, and I am using BioPerl to try and do something that I think should be rather simple (famous last words!). Basically I have a list of genes (~5000) and I want to search the upstream sequence of those genes for the presence of a particular transcription factor binding site (TFBS). To do this I thought I could find the genomic coordinates of the gene, which I managed using EntrezGene and extracting the from and to coordinates from the url. (wiki here) . Now I need to find a way to actually get the upstream sequence (start_pos - 3500 .. start_pos + 100). I have tried the example given in the BioPerl wiki (wiki here) but it isn't working for me and I am not really sure as to why, or what to try next. If any of you have any ideas, I would be very grateful. Thanks for helping a total noob out. Cheers, Davy.
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