ANNOUNCE: ProMSED2 for those working with protein or DNA sequences

Alexey M. Eroshkin eroshkin at vector.nsk.su
Sun Feb 9 16:47:52 EST 1997


   ProMSED2: Protein Multiple Sequence EDitor-2 for Win 3.11/95

     State Research Center of Virology an Biotechnology "Vector"
                Institute of Molecular  Biology
          Koltsovo, Novosibirsk Region,  633159  Russia

Software package ProMSED2, an MS-Windows application for both
automatic and manual protein sequence alignment, protein
editing, comparison and analysis is available from EBI software
library: ftp://ftp.ebi.ac.uk/pub/software/dos/promsed
(as self-extracted archive).

ProMSED2 is the enhancement of ProMSED made according to user's
remarks and suggestions. ProMSED2 reads main sequence formats and
performs automatic alignments, alignment visualization and editing
and it allows sequences to be aligned interactively leaving
unchanged previously aligned regions. The program has an
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 sequence as well. The program provides flexible tool for
sequences alignment, analysis, visualization, edition and
presentation preparation.

Some details. The program does or has:
o  inputs DNA and protein sequences in NBRF/PIR, Pearson (Fasta),
   MSF (GSG), EMBL/SwissProt, Intelligenetics and CLUSTAL data
   formats;
o  has interface and functions like in others Windows applications (
   source file view, font changing, marking/unmarking,
   block selection, cut and paste, UNDO, etc.);
o  loads several sequence families in different working windows,
   adds sequences to existing alignment, combines sequences from
   different files;
o  outputs the alignment in several popular formats;
o  makes presentation quality color and black-and-white prints of
   complete alignment or any selected block;
o  saves alignment picture as Windows metafile and bitmap;
o  permits to apply automatic alignment interactively (with
   options to change the alignment parameters) to any selected part
   of sequences of marked block;
o  calculates sequence similarity of complete sequences, any selected
   subset of sequences or marked block in % and in PAM250 units (matrix
   of amino acid similarity);
o  calculates total (average for %) similarity value that is
   useful to estimate the alignment quality quantitatively.
o  sorts sequences by similarity of complete sequences and of region
   in marked block;
o  displays conserved and semiconserved positions;
o  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;
o  searches subsequences and complex sequence patterns;
o  has complete HELP;
o  much more.

Special thanks to Dr.Desmond Higgins for source code of ClustalV.

Current version is restricted in number and length of sequences.
Comments, bug reports and suggestions for new features are welcome and
should be sent by email to eroshkin at vector.nsk.su. We would be happy to
get feedback from you.

Other our programs available at the same ftp site:
--------------------------------------------------

ProAnWin: Protein structure-activity/property analysis and design of
protein engineering experiments (for MS Windows 3.x/95, alignments by
ClustalV, 3D stereo pictures, physico-chemical analysis, etc.).

ProAnalyst: Multifunctional analysis of protein sequences and structures
(MS-DOS version of ProAnWin with additional functionality: searching motifs
in peptide libraries, phenotype-genotype correlations, physico-chemical
plots, variability plots, etc.).

++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
Dr. Alexey Eroshkin               Institute of Molecular Biology
E.mail: eroshkin at vector.nsk.su    State Research Center of Virology and
Tel: +7 (3832) - 647774           Biotechnology "Vector"
Fax: +7 (3832) - 328831           Koltsovo, Novosibirsk Region 633159
                                  Russia
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++




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