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  • EXTRACT MAQ sequences?

    how to simply extract the sequences of a gene list (~1000) in FASTA format from a sequence database (~400MB) in FASTA format generated by MAQ?

  • #2
    Are you starting with a ~400MB FASTA file, containing ~1000 sequences, and you just want the list of sequence identifiers ("gene names")?

    Try something like this at the Unix command line:

    grep "^>" my_database.fasta

    That string "^>" is a regular expression meaning look for any lines starting ("^") with the greater than symbol.

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    • #3
      Thanks for reply. I actually need the IDs (headers) and sequences in FASTA format.

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      • #4
        Originally posted by johnsequence View Post
        Thanks for reply. I actually need the IDs (headers) and sequences in FASTA format.
        So you have a large FASTA file, and a list of entries you want to extract from it, to give a smaller subset as a new FASTA file? This is a very general problem, and not specific to MAQ at all.

        How is your list of identifiers stored? e.g. a text file with one id per line?

        I would suggest you write a simple script, e.g. using Perl (perhaps with BioPerl) or Python (perhaps with Biopython), or your preferred script language.



        Or, if you are happier just working at the command line, you can probably do this with EMBOSS seqret.

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        • #5
          You can use a couple of the utilities in the BLAST package from NCBI. Take your large FASTA file and create a BLAST database from it using formatdb. Then retrieve just the sequences you want from the BLASTdb using the fastacmd tool.

          Code:
          %> formatdb -i <your.FASTA.file> -p F -n <your.blast.db>
          
          %> fastacmd -d <your.blast.db> -i <your.ID.file> > <output.file>
          The first command takes your FASTA file and creates your.blast.db. The -p F tells formatdb that this is a nucleotide database. The second command extracts the FASTA formatted reads from the BLAST db based on the list of of IDs in your.ID.file.

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