/ 
SmotifCS-0.04
River stage zero No dependents
/ ClusterRankSmotifs

NAME

ClusterRankSmotifs

VERSION

Version 0.01

SYNOPSIS

Script to rank smotifs in the database by their loop signature and chemical shift difference as compared to a query smotif. Two parallel clustering and ranking methods are used: (a) cluster on the go and rank based on population (b) Joe's clusters and rank using diversity.

INPUT ARGUMENTS 1) $pdbcode : 4-letter name of the folder where the experimental chemical shift data is stored 2) $smotif : smotif number in the pdb

INPUT FILES In the <pdbcode> folder: 1) shiftcands<pdbcode><motnum>_<looplength><smotif type>.csv : Files containing results of comparing the query smotifs against the database. Each file (corresponding to each smotif) includes the number of residues compared, the chemical shift difference value, the RMSD (if structure is included), the loop length, the smotif NID, the secondary structure RMSD, secondary structure lengths, and loop structural signatures for the query and database motif and their overlap.

OUTPUT FILES In the <pdbcode> folder: 1) <pdbcode>_motifs_best_XX.csv : File containing a list of smotif candidates for each query smotif in the unknown protein 2) <pdbcode>_motifs_rmsd_XX.csv : File containing rmsds of smotif candidates for each query smotif in the unknown protein. XX = Query Smotif number.

Usage:

use ClusterRankSmotifs;

ClusterRankSmotifs ($pdb,$smotif);

EXPORT

A list of functions that can be exported. You can delete this section if you don't export anything, such as for a purely object-oriented module.

SUBROUTINES

	rank_smotifs
	findranks_by_cs_clustered
    get_cluster_on_the_go
	getseq
        checkseqblosum
        read_clusters
        get_clusters
        read_joe_clusters

rank_smotifs

Subroutine to cluster and rank the smotifs from the library based on the 
chemical difference and phi/psi signature match between the library Smotif
and the query Smotif.

findranks_by_cs_clustered

	Subroutine to cluster and rank the smotifs from the library based on the 
        chemical difference and phi/psi signature match between the library Smotif
        and the query Smotif.

getseq

	Subroutine to get the loop sequence for a given smotif by reading through the <pdbcode>.out file
    $filename = 1aab_01_8HH
    $pdbcode  = 1aab

   more 1aab/1aab.out
   Name     Chain   Type  Start   Looplength  SS1length SS2length   Sequence
   1aab.pdb A       HH    14      8           15        12          SYAFFVQTSREEHKKKHPDASVNFSEFSKKCSERW
   1aab.pdb A       HH    37      4           12        22          FSEFSKKCSERWKTMSAKEKGKFEDMAKADKARYEREM

checkseqblosum

Subroutine to find the per-residue BLOSUM62 score between two sequences

read_clusters

Subroutine to read smotif clusters obtained from get_cluster_on_the_go

get_clusters

Subroutine to get clusters using Phylip

remove_nid

It will read a two-column file with format like

brinda@everest test_brinda]$head /tmp/motifclusters Cluster4: nid_376468 Cluster6: nid_167076 Cluster7: nid_096416 nid_371611 Cluster8: nid_343341 Cluster24: nid_356687 nid_318838 nid_016570 nid_229923 nid_003768 nid_091937

nid_ will removed from the second columns and output will written 
to an output file with format like:

brinda@everest test_brinda]$head /tmp/motifclusters0 Cluster4: 376468 Cluster6: 167076 Cluster7: 096416 371611 Cluster8: nid_343341 Cluster24: 356687 318838 016570 229923 003768 091937

# Cluster8: nid_343341 
# Cluster24: nid_356687 nid_318838 nid_016570 nid_229923 nid_003768 nid_091937 

# my $cluster= ($line =~ /(Cluster\d+:)\s+/)[0];

# If you are after a single match you use a scalar in 
# list context as the L-VALUE i.e
#
# my ($cluster) = $line =~ /(Cluster\d+:)\s+/;
#
# Note if you forget the ( ) around $scalar and you get a match 
# $scalar will contain the integer value 1 so don't forget the ( ). 
# The ( ) gets you list context which you need.

read_joe_clusters

Subroutine to read Joe's Smotif cluster classification (from files)

get_cluster_on_the_go

    Subroutine to obtain Smotif clusters from the top 200 Smotifs identified using chemical shift difference. 

	Input: 
	1. 4-letter pdb code (directory where all files in the modeling pipeline are saved). 
	2. Smotif number of the query Smotif under consideration
	3. RMSD threshold for clustering Smotifs (default=2.0 A). 
	4. Array of library Smotifs sorted by chemical shift difference. 

	Output: 
	Array of upto 200 library Smotifs, ranked by a compound score obtained from
	cluster size and chemical shift difference

AUTHOR

Fiserlab Members , <andras at fiserlab.org>

BUGS

Please report any bugs or feature requests to bug-. at rt.cpan.org, or through the web interface at http://rt.cpan.org/NoAuth/ReportBug.html?Queue=.. I will be notified, and then you'll automatically be notified of progress on your bug as I make changes.

SUPPORT

You can find documentation for this module with the perldoc command.

perldoc ClusterRankSmotifs

You can also look for information at:

ACKNOWLEDGEMENTS

LICENSE AND COPYRIGHT

Copyright 2015 Fiserlab Members .

This program is free software; you can redistribute it and/or modify it under the terms of the the Artistic License (2.0). You may obtain a copy of the full license at:

http://www.perlfoundation.org/artistic_license_2_0

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This license includes the non-exclusive, worldwide, free-of-charge patent license to make, have made, use, offer to sell, sell, import and otherwise transfer the Package with respect to any patent claims licensable by the Copyright Holder that are necessarily infringed by the Package. If you institute patent litigation (including a cross-claim or counterclaim) against any party alleging that the Package constitutes direct or contributory patent infringement, then this Artistic License to you shall terminate on the date that such litigation is filed.

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