ProMSED: protein multiple sequence editor for Windows 3.11/95.

Computer applications in the biosciences : CABIOS Pub Date : 1997-06-01 DOI:10.1093/bioinformatics/13.3.243

A S Frolov, I S Pika, A M Eroshkin

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引用次数: 5

Abstract

Motivation: Most protein sequence alignment algorithms give similar results on closely related proteins, while manual intervention may be needed for distantly related molecules. To correct the alignment, it is often necessary to repeat calculations on selected parts of the alignments and edit the alignment manually. Software implementing such interactive alignment procedures is of significance.

Results: This paper presents a new MS Windows application called ProMSED for both automatic and manual protein sequence alignment. The program reads main sequence formats and has a user-friendly interface. ProMSED performs automatic (ClustalV algorithm) alignments, alignment visualization and editing, and it allows sequences to be aligned interactively leaving previously aligned regions unchanged. Manual alignment and sequence analysis are facilitated by colouring schemes reflecting amino acid similarity of mutational and physicochemical properties. The interactive alignment of a diverged set of reverse transcriptases has located four out of six known conserved motifs.

Availability: ProMSED is available on request from the authors. DEMO is available from ftp://ftp.ebi.ac.uk/pub/ software/dos/promsed/ or ftp://iubio.bio.indiana.edu/molbio/ ibmpc/.

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承诺:蛋白质多序列编辑器为Windows 3.11/95。

动机:大多数蛋白质序列比对算法在密切相关的蛋白质上给出类似的结果，而对于距离较远的分子可能需要人工干预。为了纠正对齐，通常需要对所选的对齐部分重复计算并手动编辑对齐。实现这种交互式校准过程的软件是有意义的。结果:本文提出了一个新的MS Windows应用程序ProMSED，用于自动和手动蛋白质序列比对。该程序读取主序列格式，并具有用户友好的界面。ProMSED执行自动(ClustalV算法)对齐、对齐可视化和编辑，它允许交互式地对齐序列，而不改变先前对齐的区域。通过反映突变和物理化学性质的氨基酸相似性的配色方案，可以方便地进行手动比对和序列分析。一组分散的逆转录酶的相互作用比对已经定位了六个已知保守基序中的四个。可用性:promise可根据作者的要求提供。DEMO可从ftp://ftp.ebi.ac.uk/pub/ software/dos/ committed /或ftp://iubio.bio.indiana.edu/molbio/ ibmpc/获得。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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Computer applications in the biosciences : CABIOS

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