aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity.
aLeaves facilitates on-demand exploration of metazoan gene family trees on MAFFT sequence alignment server with enhanced interactivity.
复制标题
DOI：
10.1093/nar/gkt389
复制
发表时间：
2013-07
影响因子：
14.9
通讯作者：
Katoh K
中科院分区：
文献类型：
--
作者：
Kuraku S;Zmasek CM;Nishimura O;Katoh K
我们报告了一个新的web服务器，叶片（http://aleaves.cdb.riken.jp/），从不同的动物基因组同源收集。在涉及多物种的分子比较研究中，大多数后续生物学分析都依赖于同源性鉴定。它可以通过明确的系统发育推断得到最准确的结果。越来越多的物种受到大规模测序的影响，但由此产生的资源分散在独立的基于项目的、多物种但独立的网站上。这使数据访问变得复杂，并成为分子系统发育分析全面性的严重障碍。为了克服这一困难而推出的leafes从各种数据源收集类似于输入查询序列的序列。收集到的序列可以传递到MAFFT序列比对服务器（http://mafft.cbrc.jp/alignment/server/），该服务器在交互性方面得到了显著改进。这个更新可以在(i)使用始祖鸟树查看器的序列选择，（ii）多个序列对齐和（iii）树推理之间切换。这可以作为一个循环执行，直到到达一个合理的数据集，这将最小化冗余，以便在覆盖相关分类群的同时更好地了解和处理系统发育推断。通过leaf和MAFFT之间的无缝链接实现的工作流程为解决动物学和进化生物学中的各种问题提供了方便的在线平台。
We report a new web server, aLeaves (http://aleaves.cdb.riken.jp/), for homologue collection from diverse animal genomes. In molecular comparative studies involving multiple species, orthology identification is the basis on which most subsequent biological analyses rely. It can be achieved most accurately by explicit phylogenetic inference. More and more species are subjected to large-scale sequencing, but the resultant resources are scattered in independent project-based, and multi-species, but separate, web sites. This complicates data access and is becoming a serious barrier to the comprehensiveness of molecular phylogenetic analysis. aLeaves, launched to overcome this difficulty, collects sequences similar to an input query sequence from various data sources. The collected sequences can be passed on to the MAFFT sequence alignment server (http://mafft.cbrc.jp/alignment/server/), which has been significantly improved in interactivity. This update enables to switch between (i) sequence selection using the Archaeopteryx tree viewer, (ii) multiple sequence alignment and (iii) tree inference. This can be performed as a loop until one reaches a sensible data set, which minimizes redundancy for better visibility and handling in phylogenetic inference while covering relevant taxa. The work flow achieved by the seamless link between aLeaves and MAFFT provides a convenient online platform to address various questions in zoology and evolutionary biology.
登录
查看更多内容
DOI：
10.1093/bioinformatics/8.3.275
发表时间：
1992-06-01
期刊：
COMPUTER APPLICATIONS IN THE BIOSCIENCES
影响因子：
--
作者：
JONES, DT;TAYLOR, WR;THORNTON, JM
通讯作者：
THORNTON, JM
影响因子：
14.9
作者：
Benson DA;Cavanaugh M;Clark K;Karsch-Mizrachi I;Lipman DJ;Ostell J;Sayers EW
通讯作者：
Sayers EW
影响因子：
14.9
作者：
Flicek P;Ahmed I;Amode MR;Barrell D;Beal K;Brent S;Carvalho-Silva D;Clapham P;Coates G;Fairley S;Fitzgerald S;Gil L;García-Girón C;Gordon L;Hourlier T;Hunt S;Juettemann T;Kähäri AK;Keenan S;Komorowska M;Kulesha E;Longden I;Maurel T;McLaren WM;Muffato M;Nag R;Overduin B;Pignatelli M;Pritchard B;Pritchard E;Riat HS;Ritchie GR;Ruffier M;Schuster M;Sheppard D;Sobral D;Taylor K;Thormann A;Trevanion S;White S;Wilder SP;Aken BL;Birney E;Cunningham F;Dunham I;Harrow J;Herrero J;Hubbard TJ;Johnson N;Kinsella R;Parker A;Spudich G;Yates A;Zadissa A;Searle SM
通讯作者：
Searle SM
影响因子：
3
作者：
Gouveia-Oliveira, Rodrigo;Sackett, Peter W.;Pedersen, Anders G.
通讯作者：
Pedersen, Anders G.
影响因子：
10.7
作者：
Katoh K;Standley DM
通讯作者：
Standley DM