DCSE, new multiple sequence alignment editor available (DOS,VMS,IRIX)

Peter De Rijk derijkp at reks.uia.ac.be
Wed Sep 29 09:36:01 EST 1993


[ Article crossposted from bionet.software ]
[ Author was Peter De Rijk ]
[ Posted on Wed, 29 Sep 1993 14:31:46 GMT ]


DCSE is now available via anonymous ftp on uiam3.uia.ac.be (143.169.8.1).
This server is a VAXstation running VMS. To get to the goodies, type
ftp uiam3.uia.ac.be
cd [.dcse]
and then get the version you need.

What is DCSE
------------

DCSE (Dedicated Comparative Sequence Editor) is a multiple alignment
editor. It can be used to edit protein, DNA or RNA alignments. The
structure of the molecules can be incorporated in the alignment. It is
written in C, and it uses dynamic memory for most things. This means
you can almost edit any size of alignment with it (providing you have
enough memory). When you work on a small alignment, or on a small part
of an alignment, DCSE will only use the memory necessary for this.

Some of its features:

 - colouring of bases, amino acids, and secondary structure
 - easy menu interface (also key short-cuts)
 - automatic alignment relative to sequences already aligned with others
 - sequence grouping
 - can search for sequence, complement, sequence pattern.
 - split screen
 - marker system
 - checking of primary structure
 - checking of incorporated RNA structure
 - several ways for moving bases (or AA) or blocks of bases around
 - info on composition, variability, ...
 - working on a limited set of organisms and positions
 - making a printable file
 - ASCII data files
 - multiple operating systems

Convers is a complementary program to DCSE. It supports:
 - conversion from IG Suite, Genbank, EMBL, and PIR format
 - addition of new sequences to an alignment file from several formats
 - scanning of info in reference format

What operating systems are supported
------------------------------------

On this server there are currently versions for PC(>386)/MSDOS, VAX/VMS, and
SGI/IRIX. Also supported are RISCOS/Archimedes and ULTRIX/DEC.
Distributions for these will be available later.

Files
-----

This directory contains following files/directories:

dcsepc.zip        DCSE 2.60 and Convers 2.58 distribution for PC/MSDOS
dcseVAX           DCSE 2.60 and Convers 2.58 distribution for VAX/VMS
dcseSGI           DCSE 2.60 and Convers 2.58 distribution for SGI/IRIX
manuals           manuals for DCSE 2.60 and Convers 2.57 in directory
manuals.zip       manuals in zip format
examples          examples of alignment and reference files
examples.zip      examples in zip format

files with the zip extension can be extracted on a PC by using:
pkunzip -d -o <file>.zip
in a suitable directory (e.g. c:\dcse)
You can use any other program that understands the zip format.
You must use the binary option when transferring these files.

The VAX and SGI distribution have not been compressed. You should get all files
and place them in a directory. You must use the binary option when
transferring the executables (dcse.exe and convers.exe for VAX, dcse and
convers for SGI).

examples and manuals are also a plain directories and they contain the manuals
and the example files respectively. Since these are in plain ASCII, you can
ftp them in text mode. (examples.zip must be ftp'd in binary mode!)

How to contact me
-----------------

Peter De Rijk
University of Antwerp (UIA)
Department of Biochemistry
Universiteitsplein 1
B-2610 Antwerp

tel.: 32-03-820.23.16
fax: 32-03-820.22.48
E-mail: derijkp at reks.uia.ac.be



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