BEAP
Tool Repository
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 (zhuiastate.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.
DownloadsSizeDate/Time Created
beap_v6.tar.gz 82.47 KB2011-05-17 08:29:33
legacy_ncbi_blast.tar.gz 8.35 MB2010-07-10 12:34:00

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