IPSJ Transactions on Bioinformatics
Online ISSN : 1882-6679
ISSN-L : 1882-6679
Genome Identifier: A Tool for Phylogenetic Analysis of Microbial Genomes
Yuki ShimoyamaTokumasa Horiike
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2019 Volume 12 Pages 17-20

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Abstract

Bacterial whole-genome sequences have recently become widely available via innovative and rapid progress in technologies such as high-throughput sequencing and computing. Genomes of environmental microorganisms have also been sequenced, and their number is expected to increase in the future. Typically, phylogenetic analysis is performed after genome sequencing of such organisms. 16S rRNA is a standard locus for the phylogenetic analysis of prokaryotes. However, 16S rRNA phylogenetic trees are not always reliable because of out-paralogs and horizontal gene transfer. To overcome this problem, multiple genes (or proteins) should be employed. Therefore, we developed “Genome Identifier, ” which can be used for constructing a concatenated phylogenetic tree in the form of a species tree by predicting genes from newly sequenced genomic data and collecting homologous sequences from other species.

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© 2019 by the Information Processing Society of Japan
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