README SOFTWARE NAME: Blast Extension and Assembly Program (BEAP)
VERSION: 0.6 beta (BEAP, May 9, 2011)
5.3 (BeapViewer, May 2, 2008)
AUTHORS: James E. Koltes, Zhiliang Hu, Eric Fritz and James M. Reecy
REVISION HISTORY
beap_v.0.10 May 02 2005
beap_v.0.20 May 12 2005
beap_v.0.30 Jan 25 2007
beap_v.0.40 Mar 31 2007
beap_v.0.50 Jul 17 2007
beap_v.0.52 Sep 05 2007
beap_v.0.56 Apr 05 2008
beap_v.0.60 May 11 2011
BRIEF DESCRIPTION:
The Blast Extension and Assembly Program (BEAP) is a computer program
that uses a short starting DNA fragment, often a EST or partial gene
segment, as "primer", to recursively blast nucleotide databases in an
attempt to obtain all sequences that overlaps, directly or indirectly,
with the "primer" therefore help to "extend" the length of the original
sequence for constructing a "full length" sequence for functional
analysis, or at least to obtain neighboring regions of the segment for
SNP discovery and linkage disequilibrium analysis.
PLATFORM:
Linux/unix/MacOS X/Window or other plateforms where perl and Java
are installed.
PRE-REQUESTS:
1. NCBI Blast suite (version 2.2.23) are installed and in your path.
2. X.Q. Huang's CAP3 are installed and in your path.
THE DOWNLOAD:
There are 3 parts in the tar ball:
- beap_v.0.5:
o BEAP program in a perl script.
o A command line program that requires 'netblast' and 'cap3'.
o You can change paths among other configurable parts in the 1st section
- beap_v.0.5.conf:
o BEAP configuration file read by the main program
o A plain text file you can edit to your needs
- BeapViewer5.3.jar:
o A Java .jar file you can run directly
o You can run it directly in a (Mac or PC) windows environment
INSTALLATION:
Download and unpackage the program (gunzip; tar -xf-). Identify proper
path to perl; Change 'configure' file to suit your situation -- that's
all you need to set it up.
USAGE:
Refer to "User's Manual".
http://www.animalgenome.org/bioinfo/tools/beap/userguide.html
DATA INPUT / OUTPUT:
Refer to "User's Manual".
http://www.animalgenome.org/bioinfo/tools/beap/userguide.html
GOING FURTHER:
See "Road map to BEAP":
http://www.animalgenome.org/bioinfo/tools/beap/backgrnd.html
WEB SITE:
http://www.animalgenome.org/bioinfo/tools/beap/
CONTACT:
For problems, usage, suggestions or special requests about the software,
contact Zhiliang Hu (zhu iastate.edu)
ADDITIONAL NOTES
Legacy NCBI Blast:
"legacy_ncbi_blast.tar.gz" contains a few linux binaries of old NCBI blast
executables. This is only for user's convenience if you have the right
platform to run them. We do not provide any support or advice about them.
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beap_v6.tar.gz 
