Automatic Orthologous-Protein-Clustering from Multiple Complete-Genomes by the Best Reciprocal BLAST Hits


KIPS Transactions on Software and Data Engineering, Vol. 13, No. 2, pp. 207-214, Feb. 2006
10.3745/KIPSTD.2006.13.2.207, Full Text:

Abstract

Though the number of completely sequenced genomes quickly grows in recent years, the methods to predict protein functions by homology from the genomes have not been used sufficiently. It has been a successful technique to construct an OPCs(Orthologous Protein Clusters) with the best reciprocal BLAST hits from multiple complete-genomes. But it takes time-consuming-processes to make the OPCs with manual work. We, here, propose an automatic method that clusters OPs(Orthologous Proteins) from multiple complete-genomes, which is, to be extended, based on INPARANOID which is an automatic program to detect OPs between two complete-genomes. We also prove all possible clustering mathematically.


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Cite this article
[IEEE Style]
S. S. Kim, C. S. Rhee and K. H. Ryu, "Automatic Orthologous-Protein-Clustering from Multiple Complete-Genomes by the Best Reciprocal BLAST Hits," KIPS Journal D (2001 ~ 2012) , vol. 13, no. 2, pp. 207-214, 2006. DOI: 10.3745/KIPSTD.2006.13.2.207.

[ACM Style]
Sun Shin Kim, Chung Sei Rhee, and Keun Ho Ryu. 2006. Automatic Orthologous-Protein-Clustering from Multiple Complete-Genomes by the Best Reciprocal BLAST Hits. KIPS Journal D (2001 ~ 2012) , 13, 2, (2006), 207-214. DOI: 10.3745/KIPSTD.2006.13.2.207.