PFAAT version 2.0: a tool for editing, annotating, and analyzing multiple sequence alignments.
PFAAT version 2.0: a tool for editing, annotating, and analyzing multiple sequence alignments.
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DOI：
10.1186/1471-2105-8-381
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发表时间：
2007-10-11
影响因子：
3
通讯作者：
Huang ES
中科院分区：
文献类型：
--
作者：
Caffrey DR;Dana PH;Mathur V;Ocano M;Hong EJ;Wang YE;Somaroo S;Caffrey BE;Potluri S;Huang ES
由于具有共同的祖先，同源序列在结构和功能上相似。因此，多序列比对通常被用于识别与功能相关的趋势。当这种分析与结构和系统发育分析相结合时，会特别有成效。
在此我们介绍PFAAT 2.0版的发布，这是一个用于编辑、分析和注释多序列比对的工具。对多种注释的支持是此版本的一个关键组成部分，因为它为大多数新功能提供了一个框架。序列注释可从比对和树中获取，它们通常用于标记序列或将其超链接到相关数据库。序列注释可以手动创建，也可从UniProt条目中自动提取。一旦一个多序列比对填充了序列注释，就可以通过一个复杂的搜索对话框轻松地选择和排序序列。所选序列可以使用明确模拟序列注释和残基性质之间关系的统计方法进一步分析。残基注释可从比对查看器中获取，并且通常用于指定特定残基的结合位点或性质。
残基注释也是可搜索的，并且允许人们快速选择比对列以进行进一步的序列分析，例如计算百分比同一性。其他功能包括：计算序列保守性的新算法、在Jmol中将保守性得分映射到三维结构、显示二级结构元件以及按残基组成对序列进行排序。
PFAAT提供了一个框架，终端用户可以通过注释的形式为一个蛋白质家族指定知识。这些注释可以与复杂的分析相结合，以检验与序列、结构和功能相关的假设。
By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type of analysis is particularly productive when it is combined with structural and phylogenetic analysis. Here we describe the release of PFAAT version 2.0, a tool for editing, analyzing, and annotating multiple sequence alignments. Support for multiple annotations is a key component of this release as it provides a framework for most of the new functionalities. The sequence annotations are accessible from the alignment and tree, where they are typically used to label sequences or hyperlink them to related databases. Sequence annotations can be created manually or extracted automatically from UniProt entries. Once a multiple sequence alignment is populated with sequence annotations, sequences can be easily selected and sorted through a sophisticated search dialog. The selected sequences can be further analyzed using statistical methods that explicitly model relationships between the sequence annotations and residue properties. Residue annotations are accessible from the alignment viewer and are typically used to designate binding sites or properties for a particular residue. Residue annotations are also searchable, and allow one to quickly select alignment columns for further sequence analysis, e.g. computing percent identities. Other features include: novel algorithms to compute sequence conservation, mapping conservation scores to a 3D structure in Jmol, displaying secondary structure elements, and sorting sequences by residue composition. PFAAT provides a framework whereby end-users can specify knowledge for a protein family in the form of annotation. The annotations can be combined with sophisticated analysis to test hypothesis that relate to sequence, structure and function.
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影响因子：
5.8
作者：
Zmasek, CM;Eddy, SR
通讯作者：
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作者：
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