finding flanking annotated features

[queueing]

Hi all,
I've blasted (NCBI, nblast) a few hundred short sequences from an RNA seq library using Biopython and received a large xml file as ouptut.
What I need to to next is find the flanking genomic features in the target genomes around where the hits occurred.

When the hits do not occur in an an annotated region, I will have a hit locus on the + or - strand, and I will need to search up and down the genome to find flanking features on both the + and - strands in a gff or other annotation file(I'm assuming).

Anyone have ideas about how to automate this? I use Python, bash, R.
Thanks very much.

[maxsalm]

Hi there,

if you can transform your data into BED format, you might have some luck with "closest" tool in BEDtools (http://bedtools.readthedocs.org/en/latest/). Good luck!