Institute of Molecular Biology, State Research Center of Virology an Biotechnology "Vector", Koltsovo, Novosibirsk Region, 633159 Russia
With the tremendous increasing of protein sequence data, multiple alignment is the important techniques to understand protein structure-function organization and evolution. A number of algorithms and programs for different platforms have been previously academically produced to perform multiple alignment, including CLUSTAL V and W, PILEUP, AMULT, MSA, MULTAL, ASSEMBLE, etc. ProMSED, an easy-to-use application for Widows 3.11/95 is created to facilitate protein structure-function analysis, to perform automatic and manual multiple protein sequences alignment, alignment visualization and editing. The program automatically recognizes amino acid sequences in SWISS-PROT, NBRF/PIR, Pearson (Fasta), Intelligenetics and CLUSTAL formats and has interface and the main functions similar to popular text editor Word. Automatic alignment is based on ClustalV algorithm and may be performed in different windows with up to four protein sets. The program is effective in aligning of diverged sequences; it permits to make an interactive alignment in selected protein region keeping unchanged previously found motifs or motifs aligned based on some biological reasons (e.g., known active site residues). Manual alignment and sequence analysis are facilitated by using of group operations and by the system of color-coding reflecting amino acid similarity in physico-chemical and mutational properties, secondary structure propensities, etc. Size and number of sequences have no limits others then those imposed by current computer memory. ProMSED was tested in many protein families. As an example, the alignments obtained for Cytochromes C and Cytochromes P450 (100 sequences were used in both cases) agree with consensus patterns of these protein families from PROSITE database. ProMSED can align complete set of sequences, its subset and any selected block, providing thus flexible tool for sequences analysis, visualization, editing and presentations.