Question: How to identify the bp distance of blast results to closest genes in a genome
0
gravatar for FatihSarigol
6 weeks ago by
FatihSarigol160
Durham
FatihSarigol160 wrote:

Using the blastplus output blasted against a single species genome database prepared locally, for each blast hit, I want to search the GFF annotation file to ask how far away the hit is to the closest gene in this genome.

Easy to check manually for a few hits, but I need a program that can do it automatically. I am trying to find out if loci that are under selection are close to the coding regions to make inference if they may be controlling the expression of these flanking genes. Is there already a program that does this? If not, eventually I can share the code that I'll need to write myself here..

Thanks!

blast sequence genome • 117 views
ADD COMMENTlink written 6 weeks ago by FatihSarigol160
1

What about using bedtools intersect with increasing intervals (== expand the up/downstream region of the genes gradually)?

ADD REPLYlink written 6 weeks ago by lieven.sterck8.3k
4
gravatar for Alex Reynolds
6 weeks ago by
Alex Reynolds30k
Seattle, WA USA
Alex Reynolds30k wrote:

BEDOPS gff2bed and closest-features work with BLAST output via -outfmt 6. You could use the --dist option to report the distance between the hit and its nearest element. Ref. https://bedops.readthedocs.io/en/latest/content/reference/set-operations/closest-features.html

ADD COMMENTlink modified 6 weeks ago • written 6 weeks ago by Alex Reynolds30k
1

thanks! though if you meant it works directly, probably something is odd about my blastplus version, it did require some parsing for my output format 6, but I got it to work anyway. great tool to have!

ADD REPLYlink written 5 weeks ago by FatihSarigol160
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 681 users visited in the last hour