ANNOUNCE: The SEQIO Package, version 1.1 is now Available

James Knight knight at quad.cs.ucdavis.edu
Tue Apr 2 22:44:36 EST 1996


The SEQIO package is a software package in C (or a C library, if you
prefer) which reads and writes the major biological sequence file
formats and databases.  It has been designed so that the programmer
interface is as close to the stdio library as possible, given the more
complex I/O performed by this package.

The package supports the GenBank, EMBL, Swiss-Prot, PIR/CODATA, PIR/NBRF,
FASTA, IG/Stanford, PHYLIP, Clustal and ASN.1 file formats, along with
plain text and the output produced by the FASTA programs (FASTA, TFASTA,
SSEARCH, LFASTA, LALIGN and ALIGN).  It can be compiled and used with C
and C++ programs on most of the Unix variants and Windows NT.

This message is to announce the release of version 1.1 of the SEQIO
package.  Major changes from version 1.0:

  * Added the PHYLIP, Clustal and FASTA output formats.  The NBRF format
    now conforms completely to the format for the VMS version of the PIR
    database.

  * The program was ported to Windows NT, was compiled on Solaris, and
    was compiled with g++.
  
  * Added fmtseq, a file format conversion problem that reimplements and
    extends Don Gilbert's readseq program, with a more robust interactive
    mode and with the ability to parse FASTA program output and construct
    a big alignment from the pairwise alignments.

  * Added keyword, a program which searches files and databases for
    exact and approximate matches to a fixed-width motif.

  * Converted all of the program documentation into HTML files.


The package is freely available to anyone and can be ftp'ed from the
following FTP site:

   ftp://ftp.cs.ucdavis.edu/pub/strings/seqio.tar.gz

It is a gzip'ed, tar file (181K compressed) containing the package
code and documentation files. I've also set up a web site for the
package at

   http://wwwcsif.cs.ucdavis.edu/~knight/seqio.html






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