SeqXML BioPerl support

Converting between SeqXML and other sequence formats


    Try it! Here are two programs, one for converting (almost) any sequence format to SeqXML:

            any2seqxml (download)

    and one for converting SeqXML to (almost) any sequence format:

            seqxml2any (download)

    Both require a recent version of BioPerl, which is available here. (installation instructions)

    You can also look at the code we used to convert ref proteome fasta to seqxml.

Don’t want to install BioPerl?


   There’s a quickie, “zero-install” way to get BioPerl on your system.


    1) Okay, click here to download bioperl as a zip file:

    when it's done downloading, unzip it if your computer hasn’t done it automatically. On the

    command line, you would do:


    or whatever the file is called. You should then have a folder with some ugly name like


    3) rename that to


    4) move that folder to wherever you want to keep it. I keep mine in a directory called src in my

        home directory.

    So on my computer if I go to the command line and cd to that folder and type pwd I get:


    5) in the terminal, cd to your home directory.

    6) see if you have a file named .bash_profile by typing

    ls -l ~/.bash_profile

    7) if so, open that file in your favorite editor. if the file doesn't exist, just create the file.

    8) put this line in your .bash_profile

             export PERL5LIB=/Users/dave/src/bioperl-live

    (obviously replacing my path info with wherever you chose to put bioperl)

    9) save and close your .bash_profile

  10) open a new terminal window so that the change will take effect.

  11) on the command line of the new terminal, type

               perl -e "use Bio::SeqIO;"

    If that works, then you have "installed" bioperl. Yay!


    SeqXML support is part of the official BioPerl library. Download it here or via Git.