SeqPup, a free biosequence editor is updated to a Java version

Don Gilbert gilbertd at bio.indiana.edu
Wed Aug 20 21:43:35 EST 1997

SeqPup, version 0.7, August 1997

This is the first release of the Java conversion of SeqPup.  Many of the basic
functions of prior SeqPup are included, but not all, and a few new features
have been added.  
SeqPup is a biological sequence editor and analysis program.  It includes links
to network services and external analysis programs.  It is usable on common
computer systems, including Macintosh, MS-Windows and X-Windows.  

Features include
  multiple sequence alignment and single sequence editing [i]
  read and write several sequence file formats [i]
  sequence feature editing, and marking in prints [ni]
  translate dna/amino, consensus, reverse/complement, distance functions 
  pretty print of alignments and sequences with boxed and shaded regions
  several real-application features like copy/paste, undo/redo [i]
  Internet Sequence Retrieval System (SRS) client, and NCBI-BLAST searches [n]
  This version: [n] new; [i] incomplete features

Noteably lacking in this first Java release are methods
for calling external (child) applications. This application is a 
work in progress; it has bugs. It may be useful to you as is, but 
it is still prone to problems.  A fuller release should be available
by early 1998.

Find this software at

SeqPup is written using a free and portable class application
framework called DCLAP, now converted to the new Java language. 
This Java version will work on any computer system that supports 
Java runtime 1.0.2, including Macintosh, MS Windows, and many Unix 

Java versions of other molecular biology applications built on DCLAP
will soon be updated :
   loopDloop - an RNA secondary structure display editor
   Phylodendron - a phylogenetic tree drawing application
   FlyNapp - a FlyBase Drosophila database network application

The Java language has several important aspects and some current
drawbacks for biocomputing software. I believe the drawbacks (slowness
for one) will be overcome, and the language with its toolkits and
computer industry support will bring a new robustness and rapid
application development to biocomputing.  Please try some of these 
programs and let me know if you think these are going in the
right direction.

Developers will find the source code all these applications in the
iubio:/molbio/java/source folders.  These four applications
share about 60% code.  This framework may make a useful basis
for other biocomputing applications.

-- d.gilbert--biocomputing--indiana u--bloomington--gilbertd at bio.indiana.edu

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