[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
implementations.
Both allow searching across arbitrary boundaries.
Both are free.
hjm
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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