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

    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?

  • #2
    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...

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    • #3
      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

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      • #4
        If there are no linebreaks in the sequences, then

        Code:
        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.
        savetherhino.org

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        • #5
          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

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