Question: Blast Result Matching Both Of Two Query Sequences?
2
gravatar for Richard Smith-Unna
7.1 years ago by
UK
Richard Smith-Unna130 wrote:

If two short sequences (A and B) come from the same gene, but I don't know the name of the gene or the organism, can I perform a BLAST (or similar) search to find the gene which has best similarity with BOTH A and B? That is, only return results where A and B align to the same full length sequence.

I realise I can do a BLAST/BLAT search for each and look for the matching entries, but I wondered if there was an automated way already in existence.

ADD COMMENTlink modified 7.1 years ago by Manu Prestat3.9k • written 7.1 years ago by Richard Smith-Unna130
2

"which has best homology with BOTH A and B" is wrong, should be "best similarity" ! Homology is qualitative, yes or no, cannot be higher or lower.

ADD REPLYlink written 7.1 years ago by Jan Kosinski1.6k

Good point, thanks. Question updated.

ADD REPLYlink written 7.1 years ago by Richard Smith-Unna130
8
gravatar for Damian Kao
7.1 years ago by
Damian Kao15k
USA
Damian Kao15k wrote:

One thing you can try is to concatenate A and B together and insert a '-' character between them. '-' will be considered as a gap of indeterminate length to blast.

You will have to try blasting A + '-' + B and also B + '-' + A.

ADD COMMENTlink written 7.1 years ago by Damian Kao15k
2

Inferring that your sequences are DNA, I would suggest that you also run anti-sense A + - + B and A + - + anti-B, because you may not know the orientation of these 2 queries. In general, concatenation is a neat trick in BLAST.

ADD REPLYlink written 7.1 years ago by Larry_Parnell16k

Thanks - this worked. @Larry_Parnell good point about including anti-sense.

ADD REPLYlink written 7.1 years ago by Richard Smith-Unna130
4
gravatar for Eric Fournier
7.1 years ago by
Eric Fournier1.4k
Quebec, Canada
Eric Fournier1.4k wrote:

Try Blasting for a dummy sequence containing SeqA, a string of N, then SeqB. IE, SeqANNNNNNNSeqB or SeqBNNNNNNNNSeqA. The Blast program will automatically extend the string of Ns to any arbitrary length, so you'll get results who have matches to both your sequences anywhere in the gene.

ADD COMMENTlink written 7.1 years ago by Eric Fournier1.4k

Thanks - this also worked. Great tip!

ADD REPLYlink written 7.1 years ago by Richard Smith-Unna130
1
gravatar for Manu Prestat
7.1 years ago by
Manu Prestat3.9k
Marseille, France
Manu Prestat3.9k wrote:

Another possibility was to make a blastdb from the query A blast result, and then run blast on the new blastdb with the query B.

ADD COMMENTlink written 7.1 years ago by Manu Prestat3.9k
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