Saturated BLAST

Summary
Intermediate sequence search (ISS) is a strategy for recognizing distant homologues using transitive sequences. This idea is when the similarity between two remotely homologous sequences can not be detected by normal sequence comparison, if there is an intermediate sequence with significant alignment score to both of them, their similarity can still be established.

ISS and its extension, multiple ISS, which applies more than one intermediate steps, have been proved to be sensitive and practical. However, the brute-force search, which repetitively re-runs database searching, is time-consuming and hard to be done in an automatic way. Here, we present a software with graphic user interface named Saturated BLAST, which can perform the iterated multiple intermediate sequence search more efficiently and automatically.

The Saturated BLAST package was developed under LINUX system using Perl as the programming language. Starting with a single query or a set of related sequences, Saturated BLAST runs a BLAST search, organizes the output, identifies representative as search seeds, and then repetitively takes these new seeds as queries for next generation of BLAST searches. The friendly graphic user interface and the built-in BLAST result parser, multiple alignment tools and clustering algorithms provide an easy way to edit, visualize, analyze, monitor and control the search. Besides detecting remote homology, it can be also used for maintaining protein family databases and searching for new genes in genomic databases.

Download
The Saturated BLAST is developed and tested under LINUX system (Redhat distribution 5.0 - 6.1). It can also be imported to other UNIX system, you can try it. But The develop of Windows98 version is still on the way.

Saturated BLAST is free, HERE is the current version. last version and an ancient one are still available.

Installation
The installation of Saturated BLAST is quite simple, the process includes three steps:

(1) Installation of supporting perl package.
Saturated BLAST requires two perl packages for Internet access and GUI: You need to install the "Libwww-perl" package, find it at CPAN site or its homepage at gisle.aas.no

The "Tk800*" is required. Get it through CPAN or directly from the author's site at www.ni-s.u-net.com

(2) Download and unpack the distribution.
*unpack the package in your designed direction the command:
gunzip < xblast_version_number.tar.gz | tar xvf -

(3) Modify some local definitions.
There are only two places in the perl script you need to modify.

*The first site is within "xblast.pl", when you meet the line like:
my $XBLAST_ROOT = "/usr/local/bin/xblast";
change the directory to your installation directory.

*The second is in the "blastruntool.pl", please change the directory
of your local BLAST. You will have lines like these:
my $blast_root = "/data/ncbi";
$ENV{"NCBI"} = $blast_root;
$ENV{"BLASTDB"} = "$blast_root/db";
$ENV{"BLASTMAT"} = "$blast_root/data";

If you have some problems installing Saturated BLAST, check the installation guide in user's manual. There are more detailed instructions. Or contact the author at liwz@sdsc.edu.

Please cite: "Saturated BLAST: An automated multiple intermediate sequence search used to detect distant homology."
Weizhong Li, Frederic Pio, Krzysztof Pawlowski & Adam Godzik Bioinformatics (2000) 16:1105-1110.