Comments on: Searching for poly(A) tails http://blog.malde.org/index.php/2009/12/14/searching-for-polya-tails/ bioinformatics and haskell Sun, 04 Jul 2010 19:06:47 +0000 http://wordpress.org/?v=2.9.2 hourly 1 By: ketil http://blog.malde.org/index.php/2009/12/14/searching-for-polya-tails/comment-page-1/#comment-1131 ketil Fri, 18 Dec 2009 19:26:18 +0000 http://blog.malde.org/?p=65#comment-1131 I think it should be fairly fast, although I haven't profiled it or optimized it (beyond compiling with -O :-) I did a quick test now, and on my laptop (1.3GHz Core2), it took exactly one minute to process 30K ESTs (about 23MB of sequence, and 60MB quality data). Memory use is constant at about 20MB, according to 'top' (using lazy bytestrings for the sequence and qual data -> nice streaming behavior) So: about 500 ESTs/second at the moment. With some tuning, and perhaps using multiple threads, it should be possible to make parsing integers in the quality data the bottleneck. But this is fast enough for me. I think it should be fairly fast, although I haven’t profiled it or optimized it (beyond compiling with -O :-)

I did a quick test now, and on my laptop (1.3GHz Core2), it took exactly one minute to process 30K ESTs (about 23MB of sequence, and 60MB quality data). Memory use is constant at about 20MB, according to ‘top’ (using lazy bytestrings for the sequence and qual data -> nice streaming behavior)

So: about 500 ESTs/second at the moment. With some tuning, and perhaps using multiple threads, it should be possible to make parsing integers in the quality data the bottleneck. But this is fast enough for me.

]]> By: orbitz http://blog.malde.org/index.php/2009/12/14/searching-for-polya-tails/comment-page-1/#comment-1130 orbitz Wed, 16 Dec 2009 13:08:59 +0000 http://blog.malde.org/?p=65#comment-1130 Any thoughts on performance of this or is that a non-issue? Any thoughts on performance of this or is that a non-issue?

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