ReMark: an automatic program for clustering orthologs flexibly combining a Recursive and a Markov clustering algorithms

ReMark is a fully automatic tool for clustering orthologs by combining a Recursive and a Markov clustering (MCL) algorithms. The ReMark detects and recursively clusters ortholog pairs through reciprocal BLAST best hits between multiple genomes running software program (RecursiveClustering.java) in t...

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Bibliographic Details
Published in:Bioinformatics (Oxford, England) England), 2011-06, Vol.27 (12), p.1731-1733
Main Authors: KIM, Kangseok, KIM, Wonil, KIM, Sunshin
Format: Article
Language:English
Subjects:
Algorithms
Biological and medical sciences
Cluster Analysis
Fundamental and applied biological sciences. Psychology
General aspects
Genome
Markov Chains
Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects)
Proteins - classification
Proteins - genetics
Software
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Summary:ReMark is a fully automatic tool for clustering orthologs by combining a Recursive and a Markov clustering (MCL) algorithms. The ReMark detects and recursively clusters ortholog pairs through reciprocal BLAST best hits between multiple genomes running software program (RecursiveClustering.java) in the first step. Then, it employs MCL algorithm to compute the clusters (score matrices generated from the previous step) and refines the clusters by adjusting an inflation factor running software program (MarkovClustering.java). This method has two key features. One utilizes, to get more reliable results, the diagonal scores in the matrix of the initial ortholog clusters. Another clusters orthologs flexibly through being controlled naturally by MCL with a selected inflation factor. Users can therefore select the fitting state of orthologous protein clusters by regulating the inflation factor according to their research interests. Source code for the orthologous protein clustering software is freely available for non-commercial use at http://dasan.sejong.ac.kr/~wikim/notice.html, implemented in Java 1.6 and supported on Windows and Linux.
ISSN:1367-4803
1367-4811
DOI:10.1093/bioinformatics/btr259