To: molmodel at dl.ac.uk
From: eroshkin at vector.nsk.su <Alexey Eroshkin>
Subject: ANNOUNCE: ProMSED2 for those working with protein or DNA sequences
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 is available from EBI software library:
(as self-extracted archive).
If you have access to e-mail only, the program can be obtained
via e-mail by sending the following message:
To: BITFTP at pucc.Princeton.EDU
From: YOUR E-MAIL ADDRESS
ftp ftp.ebi.ac.uk uuencode
Server will return you uuencoded program in several files.
Running UUDECODE you'll get the archive with the program.
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 (GCG), 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
+ 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.
Installed educational 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, manual and
automatic alignment, 3D mono/stereo pictures, physico-chemical
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.).
Anatoly Frolov & 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