SeqPup, a free biosequence editor is updated [Java version]
gilbertd at bio.indiana.edu
Sun Jan 18 23:44:23 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.
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
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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