SeqPup, a free biosequence editor is updated [Java version]

Don Gilbert gilbertd at bio.indiana.edu
Wed Jan 14 18:34:12 EST 1998



SeqPup, version 0.8, January 1998

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 that support the Java 1.1 runtime environment, including
Macintosh, MS-Windows and X-Windows.  

Features include
  multiple sequence alignment and single sequence editing
  read and write several sequence file formats 
  sequence feature editing, manipulation and marking in prints
  translate dna/protein, consensus, reverse/complement, and distance methods 
  pretty print of alignments and sequences with boxed and shaded regions
  Internet Sequence Retrieval System (SRS), and NCBI-BLAST searches 
  * User-definable links to external analysis programs, including
    ClustalW multiple alignment, CAP contig assembly, tacg restriction map
  * Remote program client-server interface, using CORBA protocol 
  ( * - new this version)

The major addition to this second Java release are methods
for calling external 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. 

Find this software at
  ftp://iubio.bio.indiana.edu/molbio/seqpup/java/ 
  http://iubio.bio.indiana.edu/soft/molbio/seqpup/java/

SeqPup is written using a free and portable class application
framework called DCLAP, now converted to the new Java language. 
Developers will find the source code for this application and others 
in the iubio:/molbio/java/source folder.  

If you are an administrator of GCG software for your institution and
would like to test an experimental version of the client-server
interface to SeqPup with GCG at your site, please let me know.

Comments, bug reports and suggestions are welcome and can be e-mailed to
SeqPup at Bio.Indiana.Edu.

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




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