The BioInformer nr. 3, 1998 -- SeqPup 0.8




	A publication of EMBL - Outstation Hinxton, The European Bioinformatics Institute


		SeqPup 0.8 Introduction 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. This program has undergone many changes since its origin in 1990, and will continue to grow and mature in the coming years. The current release is the second version written in the new Java programming language for portable applications. 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 This release 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. 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 source folder of the MolBio Java archives. 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. Availability SeqPup is available at the Indiana University MolBio Archives. Info supplied by: D. G. Gilbert Resources and further information Indiana University (USA) http://www.indiana.edu/ Department of Biology http://www.bio.indiana.edu/ MolBio Archives ftp://iubio.bio.indiana.edu/molbio/ SeqPup ftp site ftp://iubio.bio.indiana.edu/molbio/seqpup/java/ SeqPup documentation http://iubio.bio.indiana.edu/soft/molbio/seqpup/java/se qpup-doc.html DCLAP source code ftp://iubio.bio.indiana.edu/molbio/java/source/ External sites are not endorsed by EMBL-EBI

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