tkDCSE, the Dedicated Comparative Sequence Editor

Peter De Rijk and Rupert De Wachter

Departement Biochemie, Universiteit Antwerpen, UIA, 
Universiteitsplein 1, B-2610 Antwerp, Belgium

tkDCSE (Dedicated Comparative Sequence Editor) is a tool to help obtaining
multiple sequence alignments. It can be used to edit almost any size of
protein, DNA or RNA alignment. tkDCSE has an easy to use, yet flexible and
programmable X-windows interface with a complete on-line hypertext help
system. In tkDCSE, sequences can be aligned using a combination of automatic
and manual methods. Any part of an alignment can be automatically realigned,
and any alignment can be further refined by shifting characters or blocks of
characters after visual inspection using colours. Other features such as
pattern searching, sequence grouping and refined protection mechanisms also
aid in attaining an optimised alignment.

tkDCSE has special support for the comparative study of molecules showing a
particular spatial structure. Both RNA or protein secondary structure can be
incorporated for each sequence within the alignment through the use of
special symbols. As a stronger visual clue, structural elements can also be
coloured differently. An incorporated RNA structure can be checked for
consistency. Other functions, such as searching a complement, or the
creation of a base-pairing matrix can help in finding a plausible structure
model.

tkDCSE is currently available for IRIX on Silicon Graphics machines, Solaris
2 on Suns, and Linux on PC's. Distributions and more information can be
found on the DCSE home page at URL 

  http://www-rrna.uia.ac.be/~peter/dcse/index.html.