retrieve flanking sequences from fasta file

Question

[sgmiriuka]

Hi,

I am really new to the bioworld... looking for help in trying to get the flanking sequence from NCBI or Ensemble from a list of microRNA sequences in a fasta file. I have fasta file with the human microRNA sequences, and would like to map it and fetch the upstream and downstream flanks (i.e. about 100 bp). Tried in Biomart, successful with the hairpin sequence, but not with the mature ones. Guess that should go from a script. Great if done in biopython, but any help is welcome. thanks in advance! sgm

Answer 1

[mforde84]

http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html

You'll need the coordinate intervals (i.e., bed format file - https://genome.ucsc.edu/FAQ/FAQformat#format1). Make sure that the coordinates for the feature are consistent with the assembly you are using. If not then you can use liftOver to convert them (https://genome.ucsc.edu/cgi-bin/hgLiftOver).