Abstract
Orthologous groups are useful in the genome annotation, studies on gene evolution, and comparative genomics. However, the construction of orthologous groups is difficult to automate and takes so much time as the number of genome sequences increases. Furthermore, it is not easy to guarantee the accuracy of the automatically constructed orthologous groups. We propose an automatic orthologous group construction system for a large number of genomes. A hybrid grid computer system, consisting of 40 PCs, has been devised for fast construction of the orthologous groups from large number of genome sequences. The grid system constructs orthologous groups for 89 complete prokaryotes genomes just in a week (it takes 8 months on a single computer system). Furthermore, the system provides good extensibility for adopting new genomes in the existing orthologous groups. In the real experiment of the orthologous group constructions, more than 85% of the constructed orthologous groups coincide with those of KO (KEGG Ortholog) and COGs (Clusters of Orthologous Group of Proteins). Note that KO and COGs have been constructed manually or semi-automatically at the sacrifice of the extensibility for newly completed genomes.
This research was supported by the Program for the Training of Graduate Student in Regional Innovation which was conducted by the Ministry of Commerce, Industry and Energy of Korea Government.
This work was supported by the Regional Research Centers Program of the Ministry of Education & Human Resources Development in Korea.
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Kim, TK., Kim, KR., Oh, SK., Lee, JH., Cho, WS. (2006). A Hybrid Grid and Its Application to Orthologous Groups Clustering . In: R. Berthold, M., Glen, R.C., Fischer, I. (eds) Computational Life Sciences II. CompLife 2006. Lecture Notes in Computer Science(), vol 4216. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11875741_2
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DOI: https://doi.org/10.1007/11875741_2
Publisher Name: Springer, Berlin, Heidelberg
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