Roundup 2.0：支持超过 1800 个基因组的比较基因组学。
Roundup 2.0: enabling comparative genomics for over 1800 genomes.
机构信息
The Center for Biomedical Informatics, Harvard Medical School and Department of Pathology, Beth Israel Deaconess Medical Center, Boston MA 02115, USA.
出版信息
Bioinformatics. 2012 Mar 1;28(5):715-6. doi: 10.1093/bioinformatics/bts006. Epub 2012 Jan 13.
Abstract
UNLABELLED
Roundup is an online database of gene orthologs for over 1800 genomes, including 226 Eukaryota, 1447 Bacteria, 113 Archaea and 21 Viruses. Orthologs are inferred using the Reciprocal Smallest Distance algorithm. Users may query Roundup for single-linkage clusters of orthologous genes based on any group of genomes. Annotated query results may be viewed in a variety of ways including as clusters of orthologs and as phylogenetic profiles. Genomic results may be downloaded in formats suitable for functional as well as phylogenetic analysis, including the recent OrthoXML standard. In addition, gene IDs can be retrieved using FASTA sequence search. All source code and orthologs are freely available.
AVAILABILITY
摘要
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Roundup 是一个在线数据库，包含了超过 1800 个基因组的基因直系同源物，包括 226 个真核生物、1447 个细菌、113 个古菌和 21 个病毒。直系同源物是使用 Reciprocal Smallest Distance 算法推断出来的。用户可以根据任意一组基因组在 Roundup 中查询基于单链接聚类的直系同源基因。注释后的查询结果可以以多种方式查看，包括直系同源物聚类和系统发育分布。基因组结果可以以适合功能和系统发育分析的格式下载，包括最近的 OrthoXML 标准。此外，还可以使用 FASTA 序列搜索检索基因 ID。所有的源代码和直系同源物都是免费提供的。
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