Linked Life Data

21546394

Source:http://linkedlifedata.com/resource/pubmed/id/21546394

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
12
pubmed:dateCreated
2011-6-3
pubmed:abstractText
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. AVAILABILITY AND IMPLEMENTATION: 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.
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Jun
pubmed:issn
1367-4811
pubmed:author
pubmed:issnType
Electronic
pubmed:day
15
pubmed:volume
27
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
1731-3
pubmed:meshHeading
pubmed:year
2011
pubmed:articleTitle
ReMark: an automatic program for clustering orthologs flexibly combining a Recursive and a Markov clustering algorithms.
pubmed:affiliation
Department of Knowledge Information Security, Ajou University, Suwon, Korea.
pubmed:publicationType
Journal Article, Research Support, Non-U.S. Gov't