PlantOrDB: a genome-wide ortholog database for land plants and green algae.
PlantOrDB: a genome-wide ortholog database for land plants and green algae.
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PlantOrDB：陆地植物和绿藻的全基因组直系同源数据库
DOI：
10.1186/s12870-015-0531-4
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发表时间：
2015-06-26
影响因子：
5.3
通讯作者：
Liang C
中科院分区：
文献类型：
--
作者：
Li L;Ji G;Ye C;Shu C;Zhang J;Liang C
研究背景不同功能的基因最初是由一些祖先基因通过基因复制、突变和功能重组而产生的。直向同源基因是物种形成过程中进化而来的同源基因，而旁系同源基因是基因复制过程中进化而来的同源基因，随着基因组数据的迅速增加，在不同物种间鉴定和区分这些基因已成为功能基因组学研究的重要内容。根据序列相似性，将670个肽序列分成49，355个同源基因家族。对于每个基因家族，我们生成了一个肽序列比对和系统发育树，并确定了树内每个节点的物种形成/重复事件。对于每个节点，我们还确定并突出显示了诊断特征，这些特征有助于将新的查询序列适当添加到现有的系统发育树中，并对其最佳匹配的基因家族进行序列比对。基于所需的物种或所有物种的亚群，用户可以选择性地查看给定基因家族的系统发育树、序列比对和诊断特征。PlantOrDB不仅允许用户从系统发育树中识别直系同源物或旁系同源物，而且还提供使用相互最佳命中（RBH）成对比对方法构建的所有直系同源物。用户可以上传自己的序列以找到最匹配的基因家族，并在相关的系统发育树和序列比对中可视化他们的查询序列。 http://bioinfolab.miamioh.edu/plantordb ）是陆地植物和绿色藻类的全基因组直向同源物数据库。PlantOrDB提供了高度交互式的可视化，准确的查询分类和强大的搜索功能，可用于功能基因组研究。
BackgroundGenes with different functions are originally generated from some ancestral genes by gene duplication, mutation and functional recombination. It is widely accepted that orthologs are homologous genes evolved from speciation events while paralogs are homologous genes resulted from gene duplication events.With the rapid increase of genomic data, identifying and distinguishing these genes among different species is becoming an important part of functional genomics research.DescriptionUsing 35 plant and 6 green algal genomes from Phytozome v9, we clustered 1,291,670 peptide sequences into 49,355 homologous gene families in terms of sequence similarity. For each gene family, we have generated a peptide sequence alignment and phylogenetic tree, and identified the speciation/duplication events for every node within the tree. For each node, we also identified and highlighted diagnostic characters that facilitate appropriate addition of a new query sequence into the existing phylogenetic tree and sequence alignment of its best matched gene family. Based on a desired species or subgroup of all species, users can view the phylogenetic tree, sequence alignment and diagnostic characters for a given gene family selectively. PlantOrDB not only allows users to identify orthologs or paralogs from phylogenetic trees, but also provides all orthologs that are built using Reciprocal Best Hit (RBH) pairwise alignment method. Users can upload their own sequences to find the best matched gene families, and visualize their query sequences within the relevant phylogenetic trees and sequence alignments.ConclusionPlantOrDB ( http://bioinfolab.miamioh.edu/plantordb ) is a genome-wide ortholog database for land plants and green algae. PlantOrDB offers highly interactive visualization, accurate query classification and powerful search functions useful for functional genomic research.
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影响因子：
14.9
作者：
Huerta-Cepas J;Capella-Gutiérrez S;Pryszcz LP;Marcet-Houben M;Gabaldón T
通讯作者：
Gabaldón T
影响因子：
7.7
作者：
Sarkar, Indra Neil;Planet, Paul J.;Desalle, Rob
通讯作者：
Desalle, Rob
影响因子：
10.7
作者：
Katoh K;Standley DM
通讯作者：
Standley DM
DOI：
10.2307/2412448
发表时间：
1970-01-01
期刊：
SYSTEMATIC ZOOLOGY
影响因子：
--
作者：
FITCH, WM
通讯作者：
FITCH, WM
影响因子：
5.8
作者：
Larkin, M. A.;Blackshields, G.;Higgins, D. G.
通讯作者：
Higgins, D. G.