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Local BLAST problem (Read 4109 times)
Jan 23rd, 2013 at 10:53pm

mb   Offline
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I am having trouble with local BLAST but I'm not sure whether it is a bug or not so thought I would try here first.

I have created a BLAST database using a fasta file that is full of contigs. If I do a local BLAST on this database using one of the contigs from the original fasta file it returns the expected contig but with low sequence identity (usually 85-95%). In these cases I would expect 100% identity. I can't figure it out or see what is going on because the complete alignments are not viewable for BLAST hits...

Any idea why this is happening? If it matters I am using v 1.11.3 with Windows XP.
 
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Reply #1 - Jan 25th, 2013 at 3:57pm

Konstantin Okonechnikov   Offline
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Hi,

this looks like a bug, but I have not been able to reproduce it.

Are you using old BLAST or BLAST+? What is the size of your query contig? How many sequences are there in the database and what are the sizes?

Btw, although complete alignment is not view-able, it is possible to check the CIGAR code under "cigar" qualifier. It also may give some clue.

It would be great if you could share your data or a subset of it, so it will be possible to reproduce the bug.
 
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