Question: Can Ncbi Blast Only Search A Special Region In Database For Hits?
1
gravatar for litiancheng.gansu
6.5 years ago by
litiancheng.gansu10 wrote:

I want to blast my 36SE reads to a special region of HG19, does NCBI BLAST can do this special region search? If so, how can I do this?

for example, I only want my reads to be blasted to chr1:5000-10000 of hg19, how can I do this without creating a special small region?

ncbi blast • 1.6k views
ADD COMMENTlink modified 4 weeks ago by vkkodali1.1k • written 6.5 years ago by litiancheng.gansu10
1
gravatar for vkkodali
4 weeks ago by
vkkodali1.1k
United States
vkkodali1.1k wrote:

If you have the fasta sequence of chr1 on disk, you can use the -subject and -subject_loc options. From blastn -help:

-subject <File_In>
Subject sequence(s) to search
* Incompatible with:  db, gilist, seqidlist, negative_gilist,
db_soft_mask, db_hard_mask
-subject_loc <String>
Location on the subject sequence in 1-based offsets (Format: start-stop)
* Incompatible with:  db, gilist, seqidlist, negative_gilist,
db_soft_mask, db_hard_mask, remote
ADD COMMENTlink modified 4 weeks ago • written 4 weeks ago by vkkodali1.1k
0
gravatar for vaskin90
6.5 years ago by
vaskin90280
Milan, Italy
vaskin90280 wrote:

Why creating a small region is a problem? If you have chr1 locally on your hard drive you can open it with a sequence editor and copy the region.

ADD COMMENTlink written 6.5 years ago by vaskin90280

Yes, I can create a small region sequence database, but I don't like to because I have to convert the relative coordinate to hg19 coordinate. You may ask me why not covert relative coordinate to hg19 coordinate by add a offset, but I insist on blasting regionly because I have soon many targets regions and I have to uniform all coordinate to detect something.

ADD REPLYlink written 6.5 years ago by litiancheng.gansu10
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