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getting sequence for a list of miRNAs

hi,

I have a list of miRNAs IDs from different organisms how I can take sequence of mature miRNAs for all my IDs?

for example

lgi-mir-34

mdo-mir-193

mdo-mir-21

mdo-mir-302d

mml-mir-18

mirnas
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written by zizigolu zizigolu

2 answers

From miRBase using this file.

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written by GenoMax GenoMax

thank you, but this is whole of IDs, for example if I want only 100 IDs from which what should I do?

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written by zizigolu zizigolu

I think grep -A 1 -F -f filewithids.txt mirbase.fa would also do the trick and avoid looping.

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written by WouterDeCoster WouterDeCoster

thank you both friends

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written by zizigolu zizigolu

another way was mirdeep2

fastaselect.pl reads.fa reads_select.ids > reads_select.fa

This script only prints out the fasta entries that match an id in the id file.

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written by zizigolu zizigolu

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