Pseudofam: the pseudogene families database.
Pseudofam: the pseudogene families database.
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DOI：
10.1093/nar/gkn758
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发表时间：
2009-01
影响因子：
14.9
通讯作者：
Gerstein MB
中科院分区：
文献类型：
--
作者：
Lam HY;Khurana E;Fang G;Cayting P;Carriero N;Cheung KH;Gerstein MB
Pseudofam（pseudofam.pseudogene.org）是基于来自Pfam数据库的蛋白质家族的假基因家族的数据库。它提供了分析假基因家族结构的资源，包括查询工具，统计摘要和序列比对。当前版本的Pseudofam包含从10个真核生物基因组中鉴定的超过125000个假基因，并在近3000个家族（约占PfamA中总家族的三分之一）中进行比对。Pseudofam使用大规模并行同源性搜索算法（作为PseudoPipe管道的扩展实现）来识别假基因。每个鉴定的假基因被分配到其亲本蛋白质家族，随后通过从Pfam家族转移亲本结构域比对而彼此比对。伪基因也给出了基于本体的附加注释，反映了它们的创建模式和随后的历史。特别是，我们的注释突出了假基因家族与基因组特征的关联，如片段重复。此外，假基因家族与关键统计数据相关，这些统计数据确定了具有不寻常的假基因化程度的离群家族。统计数据还显示了家族中基因和假基因的数量如何在不同物种之间相互关联。总的来说，他们强调了这样一个事实，即持家家庭往往富含大量的假基因。
Pseudofam (http://pseudofam.pseudogene.org) is a database of pseudogene families based on the protein families from the Pfam database. It provides resources for analyzing the family structure of pseudogenes including query tools, statistical summaries and sequence alignments. The current version of Pseudofam contains more than 125 000 pseudogenes identified from 10 eukaryotic genomes and aligned within nearly 3000 families (approximately one-third of the total families in PfamA). Pseudofam uses a large-scale parallelized homology search algorithm (implemented as an extension of the PseudoPipe pipeline) to identify pseudogenes. Each identified pseudogene is assigned to its parent protein family and subsequently aligned to each other by transferring the parent domain alignments from the Pfam family. Pseudogenes are also given additional annotation based on an ontology, reflecting their mode of creation and subsequent history. In particular, our annotation highlights the association of pseudogene families with genomic features, such as segmental duplications. In addition, pseudogene families are associated with key statistics, which identify outlier families with an unusual degree of pseudogenization. The statistics also show how the number of genes and pseudogenes in families correlates across different species. Overall, they highlight the fact that housekeeping families tend to be enriched with a large number of pseudogenes.
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Pfam：氏族、网络工具和服务。
影响因子：
14.9
作者：
Finn, Robert D.;Mistry, Jaina;Schuster-Bockler, Benjamin;Griffiths-Jones, Sam;Hollich, Volker;Lassmann, Timo;Moxon, Simon;Marshall, Mhairi;Khanna, Ajay;Durbin, Richard;Eddy, Sean R.;Sonnhammer, Erik L. L.;Bateman, Alex
通讯作者：
Bateman, Alex
影响因子：
3
作者：
Gerstein, Mark;Zheng, Deyou
通讯作者：
Zheng, Deyou
影响因子：
3
作者：
Ortutay, Csaba;Vihinen, Mauno
通讯作者：
Vihinen, Mauno
影响因子：
14.9
作者：
Flicek P;Aken BL;Beal K;Ballester B;Caccamo M;Chen Y;Clarke L;Coates G;Cunningham F;Cutts T;Down T;Dyer SC;Eyre T;Fitzgerald S;Fernandez-Banet J;Gräf S;Haider S;Hammond M;Holland R;Howe KL;Howe K;Johnson N;Jenkinson A;Kähäri A;Keefe D;Kokocinski F;Kulesha E;Lawson D;Longden I;Megy K;Meidl P;Overduin B;Parker A;Pritchard B;Prlic A;Rice S;Rios D;Schuster M;Sealy I;Slater G;Smedley D;Spudich G;Trevanion S;Vilella AJ;Vogel J;White S;Wood M;Birney E;Cox T;Curwen V;Durbin R;Fernandez-Suarez XM;Herrero J;Hubbard TJ;Kasprzyk A;Proctor G;Smith J;Ureta-Vidal A;Searle S
通讯作者：
Searle S
影响因子：
14.9
作者：
Finn RD;Mistry J;Tate J;Coggill P;Heger A;Pollington JE;Gavin OL;Gunasekaran P;Ceric G;Forslund K;Holm L;Sonnhammer EL;Eddy SR;Bateman A
通讯作者：
Bateman A