Introduction
BiPad is a two-block de novo DNA motif-finding tool implemented as an iteratively greedy searching algorithm in C++ with consideration of four orientations of a two-block binding site. BiPad web interface is written in Perl script to run the motif-finder from the web server. A two-block pattern (bipartite) is consisted of two adjacent one-block motifs (i.e. half-sites) separated by flexible spacing. For example, a two-block DNA motif could be recognized by a transcription factor complex (see a homodimer binding w/ cognate two-block DNA elements). However, we define a generalized two-block motif: (i) Gap size can be specified with any number; (ii) DNA sequences of half-sites could be either homogeneous (i.e. perfect/imperfect repeats) or heterogeneous (different widths/patterns); (iii) Four orientations are locally aligned: direct repeat (DR), reversed DR (RDR), inverted repeat (IR) and everted repeat (ER) or palindrome (Pal). BiPad program searches for all the orientations and determines the best one in a so-called two-block local alignment space. BiPad is very fast as a greedy motif-finder, see a recent review in [1].

The output can be either in two-block position weight matrices(PWM) or one-block PWM. BiPad takes as input the DNA sequence file in flat text (command-line) or fasta format (web interface) and search pattern parameters including motif widths and a gap range. BiPad can function as an one-block or two-block motif-finder, and output the best alignment. In addition, the web server can display discovered motif models in graphical logos or draw logos according to user's input position frequency matrix (PFM) or PWM using Bi-Logo Plotter. Click information for instant help.

Software
Author: Dr. Chengpeng Bi (send comments to: cbi at cmh dot edu)
Compiler: GNU C++ w/ C++ STL library on Linux, Unix or MacOS
Defaults: OOPS, 19-bp one-block motif on forward strand, 10 runs, top-1 motif only.
Output: Online (default) or email
Copyright: (C) 2003-2010 Children's Mercy Hospitals, USA, All Rights Reserved

Publications
[1] A comparative study on two-block motif detection: algorithms and applications. Molecular Pharmaceutics 2008, 5, 3-16
[2] BIPAD: A web server for modeling bipartite sequence elements. BMC Bioinformatics 2006, 7, 76
[3] Bipartite pattern discovery by entropy minimization-based multiple local alignment. Nucleic Acids Res 2004, 32, 4979-4991
[4] A minimization entropy-based bipartite algorithm with application to PXR/RXRa binding sites. RECOMB 2004, pages 453-454