[BioRuby] Blast parsing speed

Yannick Wurm Yannick.Wurm at unil.ch
Sun Sep 24 13:28:53 UTC 2006

I have been happily using bioruby for the past year or so for my post- 
blast analyses. Occasionally, I will have ~ 1gb blast result files  
that need to be parsed. Here my machine may start paging and slows to  
a crawl.

Thus I wonder:
	- has anyone benchmarked bioruby, bioperl, biojava, biopython when  
processing the same file to compare speed and memory usage?
	- For the sake of future compatibility, I have been use blast's xml  
output. How much slower is it is to parse such an xml file relative  
to a "normal" or tabular blast output?



          yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne

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