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. The confidence of assembling
the resulting sequences is achieved by using a known genome, such as human genome,
as a reference.
Click here for more details.
BEAP is a Linux/Unix command line program. Basic knowledge about Unix file
system (view, edit, copy, transfer, etc) is required in order to use BEAP. The
BEAP includes a Java graphical user interface (GUI) that displays the assembled
contigs and alignments. The User's Manual is included in the software downloads
(below), and also
available on line .
Pre-request: The BEAP has built in its data pipeline the NCBI
blast tools (including blastall, megablast, netblast,
etc) and CAP3 as an
integral part of the program, therefore they are pre-requires in order to install
and run BEAP on the same platform.
Click here to download. Installation instructions are
included in the download tar ball.