Can Ncbi Blast Only Search A Special Region In Database For Hits?

Question

[litiancheng.gansu]

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?

Answer 1

[vkkodali_ncbi]

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

Answer 2

[vaskin90]

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.

[litiancheng.gansu]

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.