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
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Programs available in the readseq.jar package
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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)
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--
-- d.gilbert--bioinformatics--indiana-u--bloomington-in-47405
-- gilbertd at bio.indiana.edu
