in reply to Re^4: Bioinformatic task
in thread Bioinformatic task

Yes, of course you are absolutely right about the overhead of Bio modules and I also tend to use a simple parser myself if I know that this is only ever going to read from FASTA files. I'm just saying that trying to implement a FASTA parser yourself can be more tricky for the beginner than one might expect and trip you in unexpected ways. Anyway, I think in this case it is the comparison of sequences rather than the parsing that is the main bottleneck.

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Re^6: Bioinformatic task
by BrowserUk (Patriarch) on Nov 08, 2010 at 13:17 UTC
    in this case it is the comparison of sequences rather than the parsing that is the main bottleneck.

    Agreed, but that's no reason to add an unnecessary extra half an hour to the process :)

    Examine what is said, not who speaks -- Silence betokens consent -- Love the truth but pardon error.
    "Science is about questioning the status quo. Questioning authority".
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[reply]
      unless you want to go and get a coffee... :-)
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