Question: Positioning A Set Of ~20 Bases Dna Sequences
0
gravatar for Genotepes
8.5 years ago by
Genotepes950
Nantes (France)
Genotepes950 wrote:

Hi,

I have never used extensively BLAT, BLAST and related tools and I was wondering how to get genomic positions for a set of short DNA sequences. The goal is to identify unknown SNPs on my chip using the information given by their probe.

So if I have : seq 1 AATAGCCTCCG.. .. seq N ATTAGCCGTCAA..

I would like, as a return, a set of genomic positions: seq 1 chr n start end

Best

sequence snp • 1.5k views
ADD COMMENTlink written 8.5 years ago by Genotepes950
1
gravatar for Zev.Kronenberg
8.5 years ago by
United States
Zev.Kronenberg11k wrote:

Both Blast and Blat return exactly what you want. All you have to do is parse the output.

ADD COMMENTlink written 8.5 years ago by Zev.Kronenberg11k
0
gravatar for Genotepes
8.5 years ago by
Genotepes950
Nantes (France)
Genotepes950 wrote:

Yes you're right.

I knew it was trivial. I just wasn't able so far to find the line command that allowe ddoing this in a batch mode. I am sure it is somewhere (rtfm) but I just took my chance as I only need to this piece of knowledge and not (yet) all the things I need to know about BLAT.

Thanks,

Genotepes

ADD COMMENTlink written 8.5 years ago by Genotepes950
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