STAMP: a web tool for exploring DNA-binding motif similarities.
STAMP: a web tool for exploring DNA-binding motif similarities.
复制标题
邮票：用于探索DNA结合基序相似性的网络工具。
DOI：
10.1093/nar/gkm272
复制
发表时间：
2007-07
影响因子：
14.9
通讯作者：
Benos, Panayiotis V
中科院分区：
文献类型：
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作者：
Mahony, Shaun;Benos, Panayiotis V
STAMP是一个新开发的Web服务器，旨在支持DNA结合基序的研究。STAMP可用于针对已知基序的数据库查询基序;软件将输入基序与所选数据库（或替代地与用户提供的数据集）对齐，并返回最高得分匹配的列表。这种相似性搜索功能有望促进识别可能与新发现的基序相互作用的转录因子。当输入一个以上的基序时，STAMP还自动构建多个比对、家族结合谱和相似性树。这些功能预计将使相关的图案和固定顺序的监管模块，以及说明输入的基序集合内的相似性和冗余集的进化研究。STAMP是一个高度灵活的比对平台，允许用户在各种实施的比较指标、比对方法（本地或全局、缺口或无缺口）、多种比对策略和树构建方法之间进行“混合匹配”。基序可以作为频率矩阵（以许多常用的格式）、共有序列或已知结合位点的比对输入。STAMP还直接接受来自12个支持的基序查找器的输出文件，从而实现对基序发现分析的快速解释。STAMP可在http://www.benoslab.pitt.edu/stamp上获得
STAMP is a newly developed web server that is designed to support the study of DNA-binding motifs. STAMP may be used to query motifs against databases of known motifs; the software aligns input motifs against the chosen database (or alternatively against a user-provided dataset), and lists of the highest-scoring matches are returned. Such similarity-search functionality is expected to facilitate the identification of transcription factors that potentially interact with newly discovered motifs. STAMP also automatically builds multiple alignments, familial binding profiles and similarity trees when more than one motif is inputted. These functions are expected to enable evolutionary studies on sets of related motifs and fixed-order regulatory modules, as well as illustrating similarities and redundancies within the input motif collection. STAMP is a highly flexible alignment platform, allowing users to ‘mix-and-match’ between various implemented comparison metrics, alignment methods (local or global, gapped or ungapped), multiple alignment strategies and tree-building methods. Motifs may be inputted as frequency matrices (in many of the commonly used formats), consensus sequences, or alignments of known binding sites. STAMP also directly accepts the output files from 12 supported motif-finders, enabling quick interpretation of motif-discovery analyses. STAMP is available at http://www.benoslab.pitt.edu/stamp