PMID: 9183528Jun 1, 1997Paper

ProMSED: protein multiple sequence editor for Windows 3.11/95

Computer Applications in the Biosciences : CABIOS
A S FrolovA M Eroshkin

Abstract

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/.

Citations

May 4, 2001·Computers in Biology and Medicine·G DeléageC Geourjon
Sep 23, 2000·Journal of Biotechnology·G IgnatyevW Lubitz
Jun 16, 2012·PloS One·Amanda LaneKatherine Belov
May 31, 2001·Microbiology and Molecular Biology Reviews : MMBR·M J Jedrzejas
Sep 17, 2005·International Journal of Systematic and Evolutionary Microbiology·Abdul Majid MaszenanStephen Tiong-Lee Tay
Mar 30, 2007·International Journal of Systematic and Evolutionary Microbiology·Abdul Majid MaszenanStephen Tiong-Lee Tay
Dec 9, 2016·International Journal of Systematic and Evolutionary Microbiology·Dongwook LeeTaegun Seo

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