how to retrieve upstream sequence of a gene in cotton

Question

[dinesh]

Hello people,

I want to know how to retrieve upstream sequence of a gene.

For example, I want to blast a contig sequence to cotton genome, then can I extract upstream sequence

Answer 1

[David Langenberger]

Take the blast result and write a small script that returns the region you are interested in. In your case: 5'end of the hit and x nts upstream. Then use fastacmd to get the sequences for these regions.

[dinesh]

sir any online server

[David Langenberger]

Sorry, I don't know any cotton genome browser. And, since this is a pretty simple task when having some basic knowledge in Linux, I highly suggest to give it a try and do it yourself. It's always good to know how these things can be done. There is not always an online server with upstream regions of blast hits you created! ;)