[BiO BB] Looking for a DNA search engine that includes length as a parameter

Mike Marchywka marchywka at hotmail.com
Wed Jul 30 07:26:27 EDT 2008




> From: Lambert at Chatham.edu
> To: bbb at bioinformatics.org
> Date: Tue, 29 Jul 2008 09:08:04 -0400
> Subject: Re: [BiO BB] Looking for a DNA search engine that includes length as a parameter
>
> Thanks, Mike
>
> I've used PERL (I'll definitely take a look at BIOPERL), and could write something that locally searches downloaded FASTA results or whole genome files. I was just hoping I had missed something faster, since this is more of a side project than my main area of interest. It might be a good student project for the fall!
>

I was going to suggest that at some point it may be faster to download entire genomes and write your
own brute force or custom indexing code. 
At least on cygwin, I did find various limitations both in PERL and C++ that created important
speed problems so implementation issues could be important to getting results while
you still care or not :)  Usually it is pretty obvious that you hit an IO or virtual memory
problem and just changing format and using some bash utilities really helped ( I guess you
could store genomes in gzip format and decompress on-the-fly as one example that may be
faster than reading plain ascii files in some cases). I think with PERL the hashes are great until
they got too big for physical memory then everything pretty much stops.





> It also occurred to me (after sleeping on it) that, given the size, these might be SINEs, so I'm going to check Repeatmaster and see if I can narrow things that way.
>

>
> Mike Marchywka
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