SSMAL：使用比对图进行相似性搜索。

SSMAL: similarity searching with alignment graphs.

作者信息

Nicodème P

机构信息

INRIA-Rocquencourt and LIX Ecole Polytechnique, France; Present address: DKFZ, Abt. Theoretische Bioinformatik, INF 280, D-69120 Heidelberg, Germany.

出版信息

Bioinformatics. 1998;14(6):508-15. doi: 10.1093/bioinformatics/14.6.508.

DOI:10.1093/bioinformatics/14.6.508

PMID:9694989

Abstract

MOTIVATION

We want to provide biologists with a fast and sensitive scanning tool for searching local alignments of a protein query sequence against databases of protein multiple alignments, such as ProDom. Conversely, we want to provide a tool for locally aligning a protein multiple alignment query against a protein database such as SWISSPROT.

RESULTS

We developed the program SSMAL (Shuffling Similarities with Multiple Alignments) which utilizes features of the Blast (Altschul et al., J. Mol. Biol., 215, 403-410, 1990) algorithm and part of the Blast code. Our software allows both scanning of multiple alignments and searching with a multiple alignment. Deletions in the multiple alignment only are handled and a SSMAL search may miss some similarities found by a profile search. However, an SSMAL scan of a database such as ProDom would be 20-30 times faster that a profile scan. In the worst case, a SSMAL search is approximately 9 times faster than a profile search.

AVAILABILITY

http://www.dkfz-heidelberg.de/tbi/ people/nicodeme and follow the hyperlink SSMAL.

CONTACT

p.nicodeme@DKFZ-Heidelberg.de

摘要

动机

我们希望为生物学家提供一种快速且灵敏的扫描工具，用于在蛋白质多序列比对数据库（如ProDom）中搜索蛋白质查询序列的局部比对。相反，我们希望提供一种工具，用于将蛋白质多序列比对查询与蛋白质数据库（如SWISSPROT）进行局部比对。

结果

我们开发了程序SSMAL（多序列比对的洗牌相似度），它利用了Blast算法（Altschul等人，《分子生物学杂志》，215，403 - 410，1990）的特性和部分Blast代码。我们的软件既允许对多序列比对进行扫描，也允许使用多序列比对进行搜索。仅处理多序列比对中的缺失情况，并且SSMAL搜索可能会错过一些通过轮廓搜索发现的相似性。然而，对ProDom等数据库进行SSMAL扫描的速度比轮廓扫描快20 - 30倍。在最坏的情况下，SSMAL搜索比轮廓搜索快约9倍。