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


ProMSED2, Windows application for both automatic and manual 
DNA and protein sequence alignment, editing, comparison and 
analysis. The files required to run ProMSED are distributed in 
the form of a single compressed file. Create a directory "PROMSED" 
in your hard disk, for example, C.  Copy the file to the directory, 
run the file. To start the program run PROMSEDD.EXE from windows.

This program is provided "AS IS" without any warranty, expressed or
implied to you or any other person.  The authors will not be liable for
incidental, consequential or other damages arising through the use of
this software.  

You  can  freely copy the program and give copies to other people 
who you think might like them.

ProMSED2 is the enhancement of ProMSED made according to user's
remarks and suggestions. The program 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 sequences as well. The
program provides flexible tool for sequences alignment, analysis,
visualization, edition and presentation preparation.

The program does or has (+ - NEW or enhanced features):

+  inputs DNA and protein sequences in NBRF/PIR, Pearson (Fasta),
   MSF (GSG), EMBL/SwissProt, Intelligenetics and CLUSTAL formats;
o  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.);
o  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;
o  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;
o  has complete HELP. 

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@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, manual and 
ClustalV alignment, 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.).

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Anatoly Frolov & Alexey Eroshkin   Institute of Molecular Biology
E.mail: eroshkin@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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