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.
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VS
1 answer
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.
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.
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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