IUBio .. Biosequences .. Software .. Molbio soft .. Network News
[DIR]Parent folder
[HTML]Readseq2-help.html 13-Jun-03 38 kb
[DIR]example-programs/
[DIR]old/
[HTML]readseq-help.html 07-Jun-01 2 kb
[ ]readseq-javadocs.zip 28-May-01 174 kb
[ ]readseq-source.zip 13-May-10 613 kb
[ ]readseq.jar 13-May-10 745 kb
[ ]readseq.jsp 14-Feb-06 4 kb
[ ]test-seq.gb 06-Aug-99 101 kb
Readseq: Read & reformat biosequences

Readseq: Read & reformat biosequences .. web service

Readseq was written originally around 1989 a component of a sequence analysis program, but when I added a small, simple command-line interface, it took on a life of its own as a conversion program for bioinformatics. It's main contribution to bioinformatics is it takes on the job of guessing what your input biosequence data format is, and converting it to what your software knows how to handle. See here readseq-help.html and Readseq2-help.html for extended help.

What you need to use it is

  1. readseq.jar the java archive of this program. (don't unpack this jar on your computer).
  2. a Java runtime system on your computer, versions 1.1,1.2,1.3,1.4,1.5.
  3. for OLD MacOS 9-, take also ReadseqApp, a small Mac application to run readseq without a command line (B>do un-binhex and un-stuffit this one).

This version includes a Graphic User Interface (GUI) for those who prefer not to learn the many command line options, or who's workstation lacks a command-line interface (which probably includes most but the hardy bioinformaticians :). Double-click the readseq.jar file to launch or Run as

    java -jar readseq.jar
If you do like command line interfaces, see the docs, the brief doc is
    java -cp readseq.jar help
    java -cp readseq.jar run -- for command-line
    java -cp readseq.jar app -- for GUI application
    java -cp readseq.jar cgi -- for web CGI app

This version includes a Common Gateway Interface (CGI) for use from a web server. One web server where you can find this is IUBio Archive. See the extended help for details and installing your own readseq web cgi, or see readseq.jsp for web JSP.

This version also includes the same old Command Line Interface (CLI) that the 1992 version supported, so you can drop it in place of the older, slower, bugger, less functional Readseq from that decade.

Programmers will find the source code here also, in readseq-source.zip, with JavaDoc generated documents in readseq-javadocs.zip.
You will find a nearly identical source version bundled with other iubio java source. This is split into java 1.3/javac-compatible source code (one public class/file, file name == public class name) at this folder,
http://iubio.bio.indiana.edu/soft/molbio/java/source/ as iubio-javalib.tar.gz
with expectation in summer 2002 this will become reference readseq source.

Home of this package is http://iubio.bio.indiana.edu/soft/molbio/readseq/java/

Anyone can use Readseq. There are no copyright restrictions, it is in the PUBLIC DOMAIN.

-- Don Gilbert
software@bio.indiana.edu, May 2001
Bioinformatics group, Biology Department & Cntr. Genomics & Bioinformatics,
Indiana University, Bloomington, Indiana