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.

---

---

Posts are HTML formatted. Put <p> </p> tags around your paragraphs. Put <code> </code> tags around your code and data!

Titles consisting of a single word are discouraged, and in most cases are disallowed outright.

Read Where should I post X? if you're not absolutely sure you're posting in the right place.

Please read these before you post! —

• How do I compose an effective node title?
• How do I post a question effectively?
• Markup in the Monastery

Posts may use any of the Perl Monks Approved HTML tags:

a, abbr, b, big, blockquote, br, caption, center, col, colgroup, dd, del, details, div, dl, dt, em, font, h1, h2, h3, h4, h5, h6, hr, i, ins, li, ol, p, pre, readmore, small, span, spoiler, strike, strong, sub, summary, sup, table, tbody, td, tfoot, th, thead, tr, tt, u, ul, wbr

You may need to use entities for some characters, as follows. (Exception: Within code tags, you can put the characters literally.)

	For:		Use:
	&		&
	<		&lt;
	>		&gt;
	[		&#91;
	]		&#93;

Link using PerlMonks shortcuts! What shortcuts can I use for linking?

See Writeup Formatting Tips and other pages linked from there for more info.