Announce: NHGRI's WebBLAST 2.00.5 Beta1

josephryan at yahoo.com josephryan at yahoo.com
Thu Dec 3 22:51:22 EST 1998

NHGRI's WebBLAST 2.00.5 Beta1

NHGRI's Computational Genomics Core is pleased to announce the first
Beta release of WebBLAST2.

Special Note

WebBLAST2 is software.  It runs on UNIX server and is used to organize,
analyze and annotate sequence data.  WebBLAST2 is not a public server
like NCBI's frontend to BLAST.


WebBLAST2 is available for download from
While WebBLAST is in Beta, we require that you register before downloading.


In order to install and use this package you will need Perl version
5.004 or better.  We recommend that you have the following packages
installed before you install WebBLAST:

1. NHGRI::Blastall.pm Version 0.22 or better

2. NCBI's local BLAST Version 2.0.6 or better
   (for help installing NCBI's local BLAST see

3. SequenceUpload
   WebBLAST2 includes a MAC Droplet which is designed to simplify the process
   of transferring sequences to the Unix server from a Macintosh
   (connected to a sequencer).  This package is bundled separately.

4. Staden (OPTIONAL)
   WebBLAST2 includes a Java Applet which allows one to examine Trace files.
   This Applet requires that Staden be installed on the same machine as the
   web server.  If you do not have Staden the TraceViewer will not work
   but everything else will.


WebBLAST2 is a complete rewrite of WebBLAST1.  Changes in this version
include the dependancy on NCBI BLAST2 rather than NCBI BLAST1.
Much of the code has been encapsulated in the NHGRI::Blastall module
which allows for simpler bugfixes.  While WebBLAST1 used the auto-blast.plx
script for BLASTing only and used stat-blast.plx for parsing reports,
WebBLAST2 has combined both functionalities into auto-blast.plx.
WebBLAST2 includes support for multiple projects allowing for the
same binaries to support different sequencing efforts.  auto-blast.plx
allows for a project configuration file which allows for different
BLAST runs and cutoff criteria for different projects.  A Graphical
Viewer Applet has been added to the web display.   A TraceViewer,
developed at Whitehead Institute for Biomedical Research by Michael Zody,
has been added to the web display.  The Sequence Uploader has added support
for projects as well as display menus which allow for better more accurate
file transfer.


Support is offered in the form of a mailing list.  Questions about how to
install and use WebBLAST should be directed to the web-blast-help mailing
list .  You can join the mailing list by sending a message to
majordomo at nhgri.nih.gov with the following command in the body of your
email message:

    subscribe webblast-help

More Info

There is more information available on the WebBLAST web site.


Public Domain Notice

This software/database is "United States Government Work" under the terms
of the United States Copyright Act. It was written as part of the authors'
official duties for the United States Government and thus cannot be
copyrighted. This software/database is freely available to the public for
use without a copyright notice. Restrictions cannot be placed on its present
or future use.

Although all reasonable efforts have been taken to ensure the accuracy
and reliability of the software and data, the National Human Genome
Research Institute (NHGRI) and the U.S. Government does not and cannot
warrant the performance or results that may be obtained by using this
software or data. NHGRI and the U.S. Government disclaims all warranties
as to performance, merchantability or fitness for any particular purpose.

In any work or product derived from this material, proper attribution
of the authors as the source of the software or data should be made, using
http://genome.nhgri.nih.gov/webblast as the citation.


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