HmtDB, a Human Mitochondrial Genomic resource based on variability studies supporting population genetics and biomedical research
HmtDB, a Human Mitochondrial Genomic resource based on variability studies supporting population genetics and biomedical research
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DOI：
10.1186/1471-2105-6-s4-s4
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发表时间：
2005-12-01
影响因子：
3
通讯作者：
Tommaseo-Ponzetta, M
中科院分区：
文献类型：
--
作者：
Attimonelli, M;Accetturo, M;Tommaseo-Ponzetta, M
背景：基于线粒体DNA分析和线粒体疾病研究的群体遗传学研究产生了大量的序列数据和相关信息。目前，这些数据分布在世界各地不同组织的数据库和网站中，这些数据库和网站之间没有很好地集成。此外，用户通常不可能提交并同时分析自己的数据，将其与给定数据库的内容进行比较，无论是群体遗传学还是线粒体疾病数据。结果：HmtDB 是一个集成良好的基于网络的人类线粒体生物信息资源，旨在支持群体遗传学和线粒体疾病研究，这要归功于基于位点特异性核苷酸和氨基酸变异性估计的新方法。 HmtDB 由人类线粒体基因组数据库（用群体数据注释）和一组生物信息学工具组成，能够生成位点特异性变异数据并自动表征新测序的人类线粒体基因组。用于检索基因组的查询系统和用于注释新基因组的网络提交工具已经设计并将很快实施。第一个版本包含 1255 个完整注释的人类线粒体基因组。可以下载核苷酸位点特异性变异数据和多比对基因组。还提供了对 1255 个人类基因组和 60 个哺乳动物物种的 13 个蛋白质基因编码估计的人类内和物种间氨基酸变异性数据。 HmtDB 注册后可在 http://www.hmdb.uniba.it 免费获取。结论：HmtDB 项目将有助于完成和/或完善单倍群分类，并在变异性估计的基础上揭示线粒体突变的真正致病潜力。
Background: Population genetics studies based on the analysis of mtDNA and mitochondrial disease studies have produced a huge quantity of sequence data and related information. These data are at present worldwide distributed in differently organised databases and web sites not well integrated among them. Moreover it is not generally possible for the user to submit and contemporarily analyse its own data comparing them with the content of a given database, both for population genetics and mitochondrial disease data.Results: HmtDB is a well-integrated web-based human mitochondrial bioinformatic resource aimed at supporting population genetics and mitochondrial disease studies, thanks to a new approach based on site-specific nucleotide and aminoacid variability estimation. HmtDB consists of a database of Human Mitochondrial Genomes, annotated with population data, and a set of bioinformatic tools, able to produce site-specific variability data and to automatically characterize newly sequenced human mitochondrial genomes. A query system for the retrieval of genomes and a web submission tool for the annotation of new genomes have been designed and will soon be implemented. The first release contains 1255 fully annotated human mitochondrial genomes. Nucleotide site-specific variability data and multialigned genomes can be downloaded. Intra-human and inter-species aminoacid variability data estimated on the 13 coding for proteins genes of the 1255 human genomes and 60 mammalian species are also available. HmtDB is freely available, upon registration, at http://www.hmdb.uniba.it.Conclusion: The HmtDB project will contribute towards completing and/or refining haplogroup classification and revealing the real pathogenic potential of mitochondrial mutations, on the basis of variability estimation.