Guys

I enjoyed the node. Here is a suggested topic that would be worth pursuing for the biological crowd

  • Data Structures. So BioPerl gives you some pretty cool data structures that are easy to handle. Its when you run into custom structures that you get problems. For instance if I'm working with E.coli, I have ~5e6 bp of DNA - 1e7bp if I'm working on each nucleotide on both strands. How do I manage working with an analysis that needs to annotate every base, eg working with coverage from next gen analysis. Using arrays or hashes gets ugly because you will typically run out of memory. I'm not aware of an out of the box BioPerl solution, though I could stand to be corrected. You could use pack and unpack. You could use DB::File. You might even go to Berkeley DB. But the problem is general enough that it would be useful to see one or more tutorials on what to do for these larger analysis problems that are beyond simple scripts and not necessarily part of the BioPerl toolbox.

    • MadraghRua
    yet another biologist hacking perl....

    In reply to Re: Perl and Bioinformatics by MadraghRua
    in thread Perl and Bioinformatics by biohisham

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