[BiO BB] sequence analysis

Harry Mangalam harry.mangalam at uci.edu
Fri Oct 26 20:07:11 EDT 2007

And not to start a 'grep' war, but nrgrep and agrep are also faster 
than either fgrep or grep and allow searching with errors.  nrgrep 
decays more smoothly with more complex patterns but agrep has more 
Both allow searching across arbitrary boundaries.
Both are free.

On Wednesday 24 October 2007, Dr. Christoph Gille wrote:
> You could use fgrep. Fgrep is faster than grep.
> Before, you should transform the database file such that
> each sequence takes one line without blank and without
> line breaks (using tr and sed)
> Database files are optimized for hole cards for
> historical reasons. Lines are  wrapped after at least after 72
> characters, preventing the use of fgrep.
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Harry Mangalam - Research Computing, NACS, E2148, Engineering Gateway, 
UC Irvine 92697  949 824 0084(o), 949 285 4487(c) 
harry.mangalam at uci.edu

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