A web tool for comparative genomics: G-compass

Yasuyuki Fujii, Takeshi Itoh, Ryuichi Sakate, Kanako O. Koyanagi, Akihiro Matsuya, Takuya Habara, Kaori Yamaguchi, Yayoi Kaneko, Takashi Gojobori, Tadashi Imanishi*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

In order to assist the progression of comparative genomics, we have developed a new web-based tool, named G-compass, for browsing and analysis of genome alignments. G-compass utilizes 829,311 pieces of genome alignments between human and mouse that were originally produced for this tool. The quality of the genome alignment set was evaluated by using several statistics. As a result, the alignment set is found to cover approximately 17% of the human genome and 82% of the annotated exons. The averages of nucleotide sequence identity and sequence length are 71.2% and 673.6 bp, respectively. In comparison with public data, it appeared that our data is more expansive and possesses greater genome coverage. G-compass incorporates unique functions such as window analysis of individual alignments. Furthermore, with G-compass and the joint help of H-InvDB, we were able to find highly conserved genomic segments and a human specific antisense transcript candidate, demonstrating that G-compass is useful for facilitating biological discoveries. G-compass is publicly accessible on the WWW at http://www.jbirc.aist.go.jp/g-compass/.

Original languageEnglish (US)
Pages (from-to)45-52
Number of pages8
JournalGene
Volume364
Issue number1-2
DOIs
StatePublished - Dec 30 2005

Keywords

  • Bioinformatics
  • Database
  • Evolutionary biology
  • Genome alignment
  • Genome browser
  • Orthologous gene

ASJC Scopus subject areas

  • Genetics

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