Fujii Yasuyuki, Itoh Takeshi, Sakate Ryuichi, Koyanagi Kanako O, Matsuya Akihiro, Habara Takuya, Yamaguchi Kaori, Kaneko Yayoi, Gojobori Takashi, Imanishi Tadashi
Japan Biological Information Research Center, Japan Biological Informatics Consortium, AIST Bio-IT Research Building 7F, 2-42, Aomi, Koto-ku, Tokyo, Japan.
Gene. 2005 Dec 30;364:45-52. doi: 10.1016/j.gene.2005.05.043. Epub 2005 Oct 5.
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/.
为了推动比较基因组学的发展，我们开发了一种名为G-compass的新型基于网络的工具，用于浏览和分析基因组比对。G-compass利用了最初为此工具生成的829,311条人类和小鼠之间的基因组比对数据。通过使用多种统计方法评估了基因组比对数据集的质量。结果发现，该比对数据集覆盖了约17%的人类基因组和82%的注释外显子。核苷酸序列同一性和序列长度的平均值分别为71.2%和673.6 bp。与公共数据相比，我们的数据似乎更广泛且具有更大的基因组覆盖范围。G-compass具有独特的功能，如对单个比对进行窗口分析。此外，借助G-compass以及H-InvDB的共同帮助，我们能够找到高度保守的基因组片段和一个人类特异性反义转录本候选物，这表明G-compass有助于促进生物学发现。可通过万维网在http://www.jbirc.aist.go.jp/g-compass/上公开访问G-compass。
