BiPad Server

| Run BiPad (password required) | Bi-Logo Plotter | Register Desk |

Registration Required
You are required to register before running the BiPad tool.
When your registration has been approved by the terms of the U.S. Public Health Service License (see below), you will be emailed a user ID and password. To register, please click on the above "Register Desk" link.

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 Development
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) 2003-2011 Children's Mercy Hospitals, USA, All Rights Reserved

License from U.S. Public Health Service
This software is provided by the Children's Mercy Hospital under a license of U.S. patent #5,867,402 from the U.S. Public Health Service. This software may be used only for research purposes in non-profit organizations. Nonprofit organizations may modify the software for their own internal research purposes but may not redistribute the software, or any modified versions of the software, to other parties. Nonprofit organizations may not grant network access to the software, any modified versions of the software, or to interfaces that directly or indirectly invoke the software or any modified versions of the software unless that access is restricted to their own employees and students for research purposes.

Download Software
Contact: Dr. Stephen ONeil (send request to: soneil at cmh dot edu)
Address: 2401 Gillham Road, Children's Mercy Hospitals, Kansas City, MO 64108 USA

BiPad Citations
[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

Last modified: April 18, 2011 by Charlie Bi, Children's Mercy Hospitals, Kansas City, Missouri USA