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ProMSED2
Introduction
ProMSED2 (Protein Multiple Sequence EDitor-2) is a Windows application for both automatic and manual DNA and protein sequence alignment, editing, comparison and analysis. The program reads main sequence formats and performs automatic alignments, alignment visualisation and editing and it allows sequences to be aligned interactively leaving unchanged previously aligned regions. The program has a user-friendly interface. Manual alignment and sequence analysis are facilitated by coloring schemes reflecting amino acid similarity in mutational, physico-chemical and other properties. Although ProMSED was targeted at protein sequences, it can be used on DNA sequences as well. The program provides flexible tool for sequences alignment, analysis, visualisation, editing and presentation preparation.
Features
The features of the program are:
- inputs DNA and protein sequences in NBRF/PIR, Pearson (Fasta), MSF (GSG), EMBL/SwissProt, Intelligenetics and CLUSTAL formats;
- has interface and functions like in others Windows applications (source file view, font changing, marking/unmarking, block and sequence selection, cut and paste, UNDO, etc.);
- loads several sequence families in different windows, adds sequences to existing alignment, combines sequences from various files;
- outputs the alignment in several popular formats;
- makes presentation quality color and black-and-white prints of complete alignment or any selected block;
- saves alignment picture as Windows metafile and bitmap;
- permits to apply automatic alignment interactively (with options to change the alignment parameters) to any selected part of sequences of marked block;
- calculates sequence similarity of complete sequences, of any selected sequence subset or of marked block in % and in PAM250 units (matrix of amino acid similarity);
- calculates total (average for %) sequence similarity value - an estimation of alignment quality;
- prints sequence similarity matrix;
- sorts sequences by similarity of complete sequences or marked block
- displays conserved and semiconserved positions
- has many amino acid coloring schemes aimed to facilitate manual alignment and understanding protein sequence features. Some schemes are:
EVOLUTIONARY CONSERVATIVE (reflects amino acid mutational properties), COMPLEX (similarity of amino acids in physico-chemical properties), HYDROPHOBICITY,CHARGE, BIG RESIDUES,ALPHA-HELIX, HELIX-BREAKERS, etc. The options to input user-defined schemes or change the colors of any amino acid groups are available;
searches subsequences and complex sequence patterns;
has complete help function.
Availability
The multiple sequence editor ProMSED2 is available for Windows 3.11 and Windows 95 systems via anonymous ftp at the University of Indiana. The educational version is restricted in number and length of sequences.
Information provided by: Alexey M. Eroshkin
Resources and further information
Contact information:
Anatoly Frolov & Alexey Eroshkin
Institute of Molecular Biology
State Research Center of Virology and Biotechnology "Vector"
Koltsovo, Novosibirsk Region 633159
Russia
E.mail: eroshkin@vector.nsk.su
Phone: +7 (3832) - 647774
Fax: +7 (3832) - 328831
Download ProMSED2
ftp://iubio.bio.indiana.edu/molbio/ibmpc/promsed2.exe
ftp://iubio.bio.indiana.edu/molbio/ibmpc/promsed2.readme
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