Program To Identify Repeats In Protein Sequence.

Question

[Pals]

Hello, Could anyone recommend me programs (for windows) that can identify repeated positions (involving 2-5 residues) in provided protein sequence. I would like to know for example, how many double alanines are in my sequence, if there are AXA, AXXA sites in the sequence or so on.

Thanks in advance.

Answer 1

[Niallhaslam]

I could imagine using a dotplot to look for repeated regions. Its just an alignment of the sequence against itself.

Wikipedia

Dotter Implementation

If you know the pattern you are looking for SLiMSearch2 allows you to search a sequence for matches to that sequence:

http://bioware.ucd.ie/~compass/Server_pages/slimsearch2.html You enter the motif (pattern) and limit to the sequence you are interested in. It also allows wildcards, so you could search for A.{0,10}A say, in your protein and find all instances of AA, A.A, A..A etc in that protein (please don't do that for the proteome!).

Answer 2

[Larry_Parnell]

In Windows, I would use a browser to run BLASTP of the protein against itself. Then look for the HSPs after the long, perfect alignment of self vs self. NCBI offers a BLAST version to align two sequences.

[Pals]

how simple..:)). Thanks a lot.