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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 302228122 by vanitham on Friday 22nd of August 2008 11:43:44 PM
Old 08-23-2008
Quote:
Originally Posted by era
So you want to tack on a trailing s? on the regex, I guess?

Code:
$regex =~ s/$/s?/ unless $regex =~ /[xzcs]$/;

The "unless" condition is not strictly necessary, you might want to take it out; I just wanted to highligt a possible complication. For this particular case you'd probably rather take the risk of a (highly unlikely) false positive rather than make it too sophisticated.

What if the user types in "RNA-binding proteins" as the input, do you want to normalize that back to "RNA[\s-]binding[\s-]proteins?" as well?
Hi,

No in such case it is not required.

If user enters "RNA binding protein*" in that case i have to pick up and highlight the words("RNA binding protein" and "RNA binding proteins" and "RNA-binding protein" and "RNA-binding proteins").

With regards
Vanitha
 

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LEARN ABOUT DEBIAN

clustalo

clustalo(1)							   USER COMMANDS						       clustalo(1)

NAME

       clustalo - General purpose multiple sequence alignment program for proteins

SYNOPSIS

       clustalo [-h]

DESCRIPTION

       Clustal-Omega  is a general purpose multiple sequence alignment (MSA) program for proteins. It produces high quality MSAs and is capable of
       handling data-sets of hundreds of thousands of sequences in reasonable time.

       In default mode, users give a file of sequences to be aligned and these are clustered to produce a guide tree and this is used to  guide  a
       "progressive alignment" of the sequences.  There are also facilities for aligning existing alignments to each other, aligning a sequence to
       an alignment and for using a hidden Markov model (HMM) to help guide an alignment of new sequences that are  homologous	to  the  sequences
       used to make the HMM.  This latter procedure is referred to as "external profile alignment" or EPA.

       Clustal-Omega  uses  HMMs  for  the alignment engine, based on the HHalign package from Johannes Soeding [1]. Guide trees are made using an
       enhanced version of mBed [2] which can cluster very large numbers of sequences in O(N*log(N)) time. Multiple  alignment	then  proceeds	by
       aligning larger and larger alignments using HHalign, following the clustering given by the guide tree.

       In  its	current  form  Clustal-Omega can only align protein sequences but not DNA/RNA sequences. It is envisioned that DNA/RNA will become
       available in a future version.

USAGE

       Tool usage is available in /usr/share/doc/clustalo/README.

DEVELOPMENT

       Headers and libraries are available in libclustalo-dev package.

CITING

       Sievers F, Wilm A, Dineen DG, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H,
	Remmert M, Soding J, Thompson JD, Higgins DG (2011).  Fast, scalable generation of high-quality protein multiple sequence alignments
	using Clustal Omega. Mol Syst Biol 7.

AUTHOR

       Olivier Sallou (olivier.sallou (at) irisa.fr) - Man page and packaging

       Conway Institute UCD Dublin (clustalw (at) ucd.ie) - clustalo

version 1.0.3							 December 14, 2011						       clustalo(1)
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