extraction upstream sequence of precursor microrna

Question

[najibveto]

hello i have several microrna with their mature sequences, it is from atlantic salmon and i need to get the precursor sequence for each microrna also i need the upstream sequence of 1000 not for each precursor to study possible binding sites for promoter studies. the atlantic salmon have a genome and it is annotated. is it possible to do it using some tools or should i do it manually for each microrna? thanks a lot for your help.

Answer 1

[shoujun.gu]

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

[najibveto]

thanks a lot for your help, however i didn't use bedtools before and also is it possible to blast and extract using bedtools? because the microrna are new in Atlantic salmon.