Frolov A S, Pika I S, Eroshkin A M
State Research Centre of Virology and Biotechnology Vector, Institute of Molecular Biology, Koltsovo, Russia.
Comput Appl Biosci. 1997 Jun;13(3):243-8. doi: 10.1093/bioinformatics/13.3.243.
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.
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.
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/.
大多数蛋白质序列比对算法在亲缘关系较近的蛋白质上能给出相似的结果，而对于亲缘关系较远的分子可能需要人工干预。为了校正比对结果，通常有必要对比对的选定部分重复计算并手动编辑比对。实现这种交互式比对程序的软件具有重要意义。
本文介绍了一种名为ProMSED的新的MS Windows应用程序，用于自动和手动蛋白质序列比对。该程序读取主要序列格式并具有用户友好的界面。ProMSED执行自动（ClustalV算法）比对、比对可视化和编辑，并且允许对序列进行交互式比对，而使先前比对的区域保持不变。通过反映突变和物理化学性质的氨基酸相似性的着色方案，便于进行手动比对和序列分析。一组不同的逆转录酶的交互式比对确定了六个已知保守基序中的四个。
可向作者索取ProMSED。演示版可从ftp://ftp.ebi.ac.uk/pub/ software/dos/promsed/ 或ftp://iubio.bio.indiana.edu/molbio/ ibmpc/获取。
