BiPad

:: DESCRIPTION

The Bipad Server is a web interface to predict sequence elements embedded within unaligned sequences. Either a bipartite model, consisting of a pair of one-block position weight matrices (PWM’s) with a gap distribution, or a single PWM matrix for contiguous single block motifs may be produced. The Bipad program performs multiple local alignment by entropy minimization and cyclic refinement using a stochastic greedy search strategy. The best models are refined by maximizing incremental information contents among a set of potential models with varying half site and gap lengths.

::DEVELOPER

Dr. Chengpeng Bi (send comments to: cbi at cmh dot edu)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

• Linux / MacOsX
• GNU C++ w
• C++ STL library

:: DOWNLOAD

  Contact: Dr. Stephen ONeil (send request to: soneil at cmh dot edu)

:: MORE INFORMATION

Citation

BMC Bioinformatics 2006, 7:76
BIPAD: A web server for modeling bipartite sequence elements
Chengpeng Bi and Peter K Rogan