How to Extract Multiple Sequence from Multi Fasta File by ID list

[Anti]

Hi,
I have a list of ids in .txt format and a multi fasta file with sequences. I need to extract sequences with the IDs in the list.

Can you help me, please?

[mike.t]

I think you can do that using seqret which is part of EMBOSS. According to the documentation the paramater -iquery1 can be used to specify a list of IDs, although probably not a file with IDs...

[maubp]

Do you program? You can do that with a few lines using a library like Biopython.

Alternatively, if you have a local Galaxy you could ask your admin to install one of these tools: http://toolshed.g2.bx.psu.edu/view/p...q_filter_by_id or http://toolshed.g2.bx.psu.edu/view/p...q_select_by_id

[rhinoceros]

If there are no linebreaks in the sequences, then

grep -A1 -w -f id.txt seqFile.fasta > output.fasta

should work. The ids have to be identical to the fasta headers including the greater than sign.

[GenoMax]

faSomeRecords from Kent utilities is the simplest solution (http://hgdownload.soe.ucsc.edu/admin/exe/linux.x86_64/)

More here: http://seqanswers.com/forums/showpos...0&postcount=13