Question: Recovering Positions Of Identical Matches From Multiple/ Pairwise Sequence Alignment
0
gravatar for VS
6.0 years ago by
VS710
USA
VS710 wrote:

I would like to do a pairwise/multiple sequence alignment for a gene from two/three species and then record in a separate file the exact positions of perfect identity between the sequences. Is there a tool that does this already? Or is there any option in blast/clustal that could help in recovering this information ?

Will be very thankful for your time and responses.

sequence analysis msa blast • 1.7k views
ADD COMMENTlink modified 6.0 years ago by Alex Reynolds28k • written 6.0 years ago by VS710

Have you tried GBlocks? http://molevol.cmima.csic.es/castresana/Gblocks.html I know it can extract highly conserved regions from an alignment, but not sure if you can configure it to extract only perfect matches. Edit: here is the webserver: http://www.vardb.org/vardb/analysis/gblocks.html

ADD REPLYlink modified 6.0 years ago • written 6.0 years ago by arnstrm1.7k
2
gravatar for Alex Reynolds
6.0 years ago by
Alex Reynolds28k
Seattle, WA USA
Alex Reynolds28k wrote:

BLAT can return exact matches, by filtering for results where the query and target sizes (sequence lengths) match. Perhaps you could do an EMBOSS Needle alignment with a very high gap penalty (to help push down gapped alignment results) and then use BLAT to do the sequence position lookup on aligned results.

ADD COMMENTlink written 6.0 years ago by Alex Reynolds28k

Thanks for the answer! Any particular reason you recommend EMBOSS Needle over blast with similarly high gap penalty?

ADD REPLYlink written 6.0 years ago by VS710

I think a local alignment (e.g., BLAST) won't always give you the edges of the query sequence in a search match, but global (e.g., Needleman-Wunsch) will. Because you want an exact match, you probably want those edges to match, too.

ADD REPLYlink modified 6.0 years ago • written 6.0 years ago by Alex Reynolds28k
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