Proceedings of the Korean Society for Bioinformatics Conference (한국생물정보학회:학술대회논문집)
- 2003.10a
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- Pages.183-192
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- 2003
Comparative Analysis of Large Genome in Human-Chimpanzee
인간-침팬지간 대량의 지놈서열 비교분석
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Kim, Tae-Hyung
(Interdisciplinary program of bioinformatics, Pusan National University, Dept of Biology, College of Natural Sciences, Pusan National University) ;
- Kim, Dae-Soo (Interdisciplinary program of bioinformatics, Pusan National University, Dept of Biology, College of Natural Sciences, Pusan National University) ;
- Jeon, Yeo-Jin (Interdisciplinary program of bioinformatics, Pusan National University, Dept of Biology, College of Natural Sciences, Pusan National University) ;
- Cho, Hwan-Gue (Interdisciplinary program of bioinformatics, Pusan National University, ALGORIGENE, Bioinformatics Lab. Dept. Computer Science, Pusan National University) ;
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Kim, Heui-Soo
(Interdisciplinary program of bioinformatics, Pusan National University, Dept of Biology, College of Natural Sciences, Pusan National University)
- Published : 2003.10.31
Abstract
With the availability of complete whole-genomes such as the human, mouse, fugu and chimpanzee chromosome 22, comparative analysis of large genomes from cross-species at varying evolutionary distances is considered one of a powerful approach for identifying coding and functional non-coding sequences. Here we describe a fast and efficient global alignment method especially for large genomic regions over mega bases pair. We used an approach for identifying all similarity regions by HSP (Highest Segment Pair) regions using local alignments and then large syntenic genome based on the both extension of anchors at HSP regions in two species and global conservation map. Using this alignment approach, we examined rearrangement loci in human chromosome 21 and chimpanzee chromosome 22. Finally, we extracted syntenic genome 30 Mb of human chromosome 21 with chimpanzee chromosome 22, and then identified genomic rearrangements (deletions and insertions ranging h size from 0.3 to 200 kb). Our experiment shows that all jnsertion/deletion (indel) events in excess of 300 bp within chimpanzee chromosome 22 and human chromosome 21 alignments in order to identify new insertions that had occurred over the last 7 million years of evolution. Finally we also discussed evolutionary features throughout comparative analyses of Ka/ks (non-synonymous / synonymous substitutions) rate in orthologous 119 genes of chromosome 21 and 53 genes of MHC-I class in human and chimpanzee genome.
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