I have micro-RNA sequences that I need to align specifically to Drosophilar melanogaster mature microRNA from mirbase using bowtie. Have realized the fasta sequence of mature miRNA in mirbase contain all the organisms that whose microRNAs have been sequenced and submitted. I was wondering how I can extract/or specifically use D. melanogaster as reference as opposed to using all the mature miRNAs.
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otieno43 •
A simple solution is to download the file https://mirbase.org/download/mature.fa , then open it in a text editor (for example, Notepad++) and manually copy all sequences that have "Drosophila melanogaster" in their titles to another file.
A simple solution (...) then open it in a text editor (for example, Notepad++) and manually copy all sequences that have "Drosophila melanogaster" in their titles to another file.
no, this is not a simple solution.
assuming https://mirbase.org/download/mature.fa there is only one line per sequence and there is 'Drosophila melanogaster' in each header:
wget -q -O - "https://mirbase.org/download/mature.fa" |\
grep -F 'Drosophila melanogaster' -A1 --no-group-separator > melanogaster.fa
Thank you, sorted this out.
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