Question: Program To Identify Repeats In Protein Sequence.
2
gravatar for Pals
5.4 years ago by
Pals1.3k
Finland
Pals1.3k wrote:

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.

repeats protein tool • 1.1k views
ADD COMMENTlink modified 5.4 years ago by Larry_Parnell15k • written 5.4 years ago by Pals1.3k
2
gravatar for Niallhaslam
5.4 years ago by
Niallhaslam2.3k
Dublin
Niallhaslam2.3k wrote:

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!).

ADD COMMENTlink written 5.4 years ago by Niallhaslam2.3k
1
gravatar for Larry_Parnell
5.4 years ago by
Larry_Parnell15k
Boston, MA USA
Larry_Parnell15k wrote:

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.

ADD COMMENTlink written 5.4 years ago by Larry_Parnell15k

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

ADD REPLYlink written 5.4 years ago by Pals1.3k
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