Readseq, biosequence format conversion tool, version 2.0.3

Don Gilbert gilbertd at bio.indiana.edu
Wed Aug 18 21:11:07 EST 1999


  Readseq version 2.0.3 (16 August 1999)

  Readseq is a program to read & reformat biosequences, and a package
  of methods for programmmers to incorporate into their software
  for this end.  This program is designed to automatically detect 
  input sequence format, and produce output formats compatible
  with different sequence analysis software.
  
  Version 2 adds the ability to parse and translate documentation
  and feature tables found in GenBank and EMBL formats, as well
  as extract sequence based on features.  A simple graphic user 
  interface is included, for use without learning command-line 
  options.   Also included is a CGI interface for web servers.  
  This is version is written in the Java language, and source code
  is freely available.
  
  Home of this package
    http://iubio.bio.indiana.edu/soft/molbio/readseq/java/
  An instance of the Web form for this is at
     http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi 

  --------------------
  Programs available in the readseq.jar package 
  --------------------
  For the current help document, use a Java Runtime command of
    jre -cp readseq.jar help 
  
  Graphic interface to Readseq (using Java swing)
    Usage:   jre -cp readseq.jar:swingall.jar iubio.readseq.app
    Macintosh users: See also Readseq.macapp, a small Mac application
    to launch readseq.jar without a command-line.
  
  HTTP server common gateway interface to Readseq
    Web servers can run this program to provide biosequence conversion.
    See for example http://iubio.bio.indiana.edu/cgi-bin/readseq.cgi
    See the help document for usage information
  
  Command line version ('classic' Readseq options are supported)
    Usage: jre -cp readseq.jar run [options] input-file(s)
  
  Options include selection among several output formats,
  selecting sequence entries from many, extracting or removing
  sequence of features listed in feature tables,  translating bases,  
  and others.  A pretty print option offers styles for alignment
  listings.

  Known biosequence formats:
 ID  Name             Read  Write  Int'leaf  Document  
  1  IG|Stanford      yes    yes        --        --   
  2  GenBank|GB       yes    yes        --       yes   
  3  NBRF             yes    yes        --        --  
  4  EMBL             yes    yes        --       yes  
  5  GCG              yes    yes        --        --  
  6  DNAStrider       yes    yes        --        -- 
  7  Fitch             --     --        --        --  
  8  Pearson|Fasta    yes    yes        --        --   
  9  Zuker             --     --        --        --  
 10  Olsen             --     --       yes        --  
 11  Phylip3.2        yes    yes       yes        --  
 12  Phylip|Phylip4   yes    yes       yes        --  
 13  Plain|Raw        yes    yes        --        --  
 14  PIR|CODATA       yes    yes        --        --  
 15  MSF              yes    yes       yes        -- 
 16  ASN.1             --     --        --        --  
 17  PAUP|NEXUS       yes    yes       yes        --  
 18  Pretty            --    yes       yes        --  
 19  BLAST            yes     --       yes        --  
 20  XML              yes    yes        --       yes   
   (Int'leaf = interleaved format; Document = documentation is parsed)
  --------------------

--
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd at bio.indiana.edu




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