SeqPup biosequence editor now includes ABI,SCF data analyses

Don Gilbert gilbertd at sunflower.bio.indiana.edu
Fri Jul 5 05:09:17 EST 1996


With the growing popularity and availability of automated sequencers,
I recently learned that there may be a need for more software for
reading, editing and assembling data from them, especially
free, multiple-platform software.    The new release of SeqPup
provides the beginnings of a bare-bones tool for analyzing
ABI and SCF format autosequencer data.  It uses Reece Hart's nice
program 'autoseq' for reading traces and calling bases.  There
are some added functions in SeqPup to allow trace display and editing 
of called bases.  CAP software by Xiaoqiu Huang is used to assembly 
sequencer sections.

At this release, SeqPup may not yet be ready for the
average biologist interested in autosequencer analyses.  But
I would like to hear from those trying it what problems you
have and what improvements you think are important to make it
into a program that can handle such functions.

-- Don


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
	
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)

[-- see bionet.software or the iubio server for some more details --]

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




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