orthoMCL (ortholog Groups of Protein Sequences) #

진화론적인 입장에서 서열의 유사성을 근거로한 종간의 동일 기능 유전자를 grouping한 데이터베이스

Data summary #

1. Genomes : 150
2. Protein sequences : 1,398,546
3. Ortholog groups : 124,740

Latest version #

1. 2015-02-19 : Letter to the EuPathDB Community
2. 2013-05-10 : OrthoMCL 5 strategies-wDK version released (beta)

Algorithm #

1. blast를 통한 서열 유사성 검사
2. 종간 reciprocal match 검사
3. 최소 3종간의 triangle 형성시 cluster 형성

Method #

1. All-v-all BLASTP of the proteins
2. Compute percent match length (query, subject lenth, HSP length, etc.)
3. Apply thresholds to blast result (E-value < 1e-5/ match length fraction >= 50%)
4. Find potential inparalog
5. Use the MCL program to cluster the pairs into groups

< Flow chart of the orthMCL algorithm for clustering ortholus proteins. >

Requirement & install #

1. MySQL

   $yum -y install mysql-server
   

2. MCL install

   $wget http://www.micans.org/mcl/src/mcl-latest.tar.gz
   

3. install

   $ ./configure --prefix=/src/MCL/mcl-14-137
   $ make
   $ make check
   $ make install
   

Reference #

1. Li Li, Christian J. Stoeckert, Jr., and David S.Roos1 (2003 ) OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes Genome Res. Sep;13(9):2178-89. (http://genome.cshlp.org/content/13/9/2178.full)

Incoming Links #

Related Bioinformaticses (Bioinformatics 0) #

• Ks로살펴본나팔꽃의진화