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Full Discussion: How to get exact match sentences?
Top Forums Shell Programming and Scripting How to get exact match sentences? Post 302225601 by vanitham on Saturday 16th of August 2008 12:23:05 AM
Old 08-16-2008
How to get exact match sentences?
Hi,

I have sentences like this:

Code:
$sent=

Protein modeling studies reveal that the RG-rich region is part of a three to four strand antiparallel beta-sheet, which in other RNA binding protein functions as a platform for nucleic acid interactions.

Heterogeneous nuclear ribonucleoparticle (hnRNP) proteins form a family of RNA binding proteins (RBPs) that coat nascent pre-mRNAs.

Finally, we have found that Pumilio2, a member of the PUF family of RNA-binding proteins, is highly concentrated at the vertebrate neuromuscular junction.

PUF proteins comprise a highly conserved family of sequence-specific RNA-binding protein that regulate target mRNAs.

User enters a query term like this "RNA binding protein" and i am taking like this.

Code:
$word=param('query');
print "\n$word\n";

What i want to do is it should pick up the sentences which has RNA-binding protein also!!

How to write a regular expression such that $word has to pick up these sentences which has "RNA-binding protein" and RNA binding protein?

With regards
Archana
 

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LEARN ABOUT DEBIAN

cm2hmmsearch

cmsearch(1)							  Infernal Manual						       cmsearch(1)

NAME

       cmsearch - search a sequence database for RNAs homologous to a CM,
	      using an HMM as a pre-filtering step to increase speed.

SYNOPSIS

       cmsearch window length score threshold cmfile compact-type HMM expanded-type HMM seqfile runsearch

DESCRIPTION

       cm2hmmsearch  uses  the	covariance  model (CM) in cmfile to search for homologous RNAs in seqfile, and outputs high-scoring alignments.  A
       compact-type HMM and/or expanded-type HMM is used as a pre-filtering step, which usually increases the overall speed of the  search.   HMMs
       created with cm2hmm are rigorous, meaning that no new false negatives are introduced by using the filter.

       The sequence file is assumed to be in FASTA format.

       CM  files are profiles of RNA consensus secondary structure. A CM file is produced by the cmbuild program, from a given RNA sequence align-
       ment of known consensus structure.

       HMM files are profiles of RNA consensus primary sequence, produced by cm2hmm from a given CM file.

OPTIONS

       --help Print brief help; includes summary of parameters.

       window length

       score threshold

       runsearch
	      Indicate whether cmsearch should actually be run.  1 will run the cmsearch and output hits.  0 will report on the filtering fraction
	      that was achieved with the HMM filters.

SEE ALSO

       For  complete  documentation,  see  the	User's	Guide  (Userguide.pdf)	that  came  with  the  distribution; or see the Infernal web page,
       http://infernal.janelia.org/.

COPYRIGHT

       Copyright (C) 2009 HHMI Janelia Farm Research Campus.
       Freely distributed under the GNU General Public License (GPLv3).
       See the file COPYING that came with the source for details on redistribution conditions.

AUTHOR

       Eric Nawrocki, Diana Kolbe, and Sean Eddy
       HHMI Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147
       http://selab.janelia.org/

Infernal 1.0.2							   October 2009 						       cmsearch(1)
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