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  • queueing
    Junior Member
    • Mar 2015
    • 4

    finding flanking annotated features

    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
    Member
    • Feb 2015
    • 18

    #2
    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!

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