Positioning A Set Of ~20 Bases Dna Sequences

Question

[Genotepes]

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

Answer 1

[Zev.Kronenberg]

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

Answer 2

[Genotepes]

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

[Leonor Palmeira]

http://www.ncbi.nlm.nih.gov/books/NBK1763/ and http://genome.ucsc.edu/goldenPath/help/blatSpec.html