SeqPup, biosequence editor & analysis platform, version 0.6

Don Gilbert gilbertd at sunflower.bio.indiana.edu
Tue Jul 2 08:17:47 EST 1996


SeqPup, version 0.6 development release, June/July 1996

New in this release:
	Easily use GCG and other command-line software over network
	Bare-bones autosequencer (ABI,SCF) base calling, editing, assembly
	Expanded sequence size limits (now can open 1.9MB H.flu genome)
	Numerous bug fixes and improvements
	
Summary

SeqPup is a biological sequence editor and analysis program
usable on the common computer systems of Macintosh,
MS-Windows and X-Windows.  It includes links to network
services and external analysis programs.

Features include
   + multiple sequence alignment and single sequence editors
   - read and write several sequence file formats
   + easy hand alignment features including colored bases and sliding
   * Internet sequence analysis services by BOP and email methods 
   - automatic multiple sequence alignment with ClustalW app
   - automatic gel fragment alignment to contigs with CAP app
   * automatic base calling from ABI or SCF trace files with autoseq app
   - phylogenetic analysis of alignments with fastDNAml and LSADT apps
   - consensus, reverse, complement, degap, and distance/similarity operations
   - restriction maps
   + pretty print of alignments and sequences with boxed and shaded regions.
   - translate dna to/from protein using various codon tables
   + find strings and ORFs
   - automatic preference saving
   - user-definable links to external analysis programs
	 (* new, + updated)

NOTICE:  This release is still unfinish, and has bugs. It may
be useful to you as is, but be warned that it is still prone
to problems.

SeqPup is being written using DCLAP, a free and portable C++ 
class application framework.  DCLAP is founded on the
NCBI Toolkit, especially it's Vibrant user-interface section
written primarily by Jonathan Kans.   SeqApp/SeqPup was
started in 1990 as sequence editor/analysis platform on
which analysis programs from other authors could be easily
incorporated into a useable interface.  

You can obtain this release thru anonymous ftp, gopher or
http to iubio.bio.indiana.edu, in folder /molbio/seqpup.
Versions are available for Macintosh (PowerMac and 68K), 
MS Windows (Win95, WinNT and Win3), and Unix/XWindows systems
including Sun Solaris, SGI Irix, DEC Unix, Linux.   The Internet 
locators to this software are

  <ftp://iubio.bio.indiana.edu/molbio/seqpup/>
  <gopher://iubio.bio.indiana.edu/11/IUBio-Software+Data/molbio/seqpup/>
  <http://iubio.bio.indiana.edu/1/IUBio-Software%2bData/molbio/seqpup/>

Source code for this software is at
  <ftp://iubio.bio.indiana.edu/util/dclap/source/>.
The bopper source for installed a server for SeqPup Internet BOP
functions is in this same folder as
  <ftp://iubio.bio.indiana.edu/util/dclap/source/bopper.tar.gz>

Comments, bug reports and suggestions for new features (see
below) are very welcome and should be sent via e-mail to
<mailto://SeqPup@Bio.Indiana.Edu/>.

June/July 96: version 0.6d release
+ "bopper" Internet protocol for client/server use of command line 
  programs such as the GCG suite.  
+ autoseq base calling app for reading ABI and SCF sequencer trace 
  file data, plus base/trace editing functions.
+ Started expanding maximum sequence limit to 2 megabases (from about 30Kb), 
  however most functions beyond viewing will still fail for >30Kb sequences.
+ Several bug fixes are included for mac, mswin, unix.  Added background 
  color in align view, minimum ORF size pref, improved tracking of changed 
  data, improved align editing, save pretty print to PICT or text; fixed 
  child app bugs; fixed mswin edit truncation to 255 bases; editable data 
  tables in selection dialogs

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




More information about the Bio-soft mailing list