PoSSuM / PoSSuMsearch 2.0 – Matching of PPSSMs using Enhanced Suffix Arrays

PoSSuM / PoSSuMsearch 2.0

:: DESCRIPTION

PoSSuM / PoSSuMsearch is a software which significant speedup of database searches with HMMs by search space reduction with PSSM (position specific scoring matrices) family model.

::DEVELOPER

JUNIOR RESEARCH GROUP FOR APPLICATION ORIENTED BIOINFORMATICS

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / SUN solaris

:: DOWNLOAD

PoSSuM / PoSSuMsearch

:: MORE INFORMATION

Citation

Michael Beckstette, Robert Homann, Robert Giegerich, and Stefan Kurtz
Significant speedup of database searches with HMMs by search space reduction with PSSM family models
Bioinformatics, 15 December 2009; 25: 3251 – 3258.

Possum – Detect Cis-elements in DNA Sequences

Possum

:: DESCRIPTION

Possum predicts cis-elements in DNA sequences using the standard method of Position Specific Scoring Matrices. It measures the resemblance of every sequence fragment to the chosen cis-element matrices by calculating log-likelihood ratio scores (base e), and returns high-scoring sequence fragments.

::DEVELOPER

Zlab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C++ Compiler

:: DOWNLOAD

 Possum

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W420-3.
MotifViz: an analysis and visualization tool for motif discovery.
Fu Y, Frith MC, Haverty PM, Weng Z.