getting sequence for a list of miRNAs

Question

[zizigolu]

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

Answer 1

[GenoMax]

From miRBase using this file.

[zizigolu]

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

[GenoMax]

grep -A 1 your_ID them out of the miRBase file using a loop OR use filterbyname.sh from BBMap OR use samtools faidx as described here: A: How To Extract A Sequence From A Big (6Gb) Multifasta File ?.

[WouterDeCoster]

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

[zizigolu]

thank you both friends

Answer 2

[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.