Tag: Find Motif

GAME – Utilize Genetic Algorithm to Find Motifs

GAME

:: DESCRIPTION

GAME (Genetic Algorithm based Motif Elicitation)is a software which utilizes a genetic algorithm to find motifs (statistically over-represented patterns) in a set of related DNA sequences. As one application, motifs could be transcription factor binding sites in a set of co-regulated genes.

::DEVELOPER

Zhi Wei

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

  GAME

:: MORE INFORMATION

Citation

Wei Z and Jensen ST,
GAME: Detecting Cis-regulatory Elements Using a Genetic Algorithm,
Bioinformatics, 2006 22:1577-1584,

Sdiscover – Tool for Finding Motifs in Sequences

Sdiscover

:: DESCRIPTION

Sdiscover is a software for discovering active (or frequently occurring) motifs in a set of protein or DNA sequences. SDISCOVERY takes a set of protein or DNA sequences and produces a collection of active motifs in the set. Another method SSORT is described that sorts the output from SDISCOVERY according to motifs’ lengths and deletes all substring motifs having the same occurrence number as their superstring motifs.

::DEVELOPER

Dr. Jason Tsong-Li Wang 

:: REQUIREMENTS

  • Linux
  • C Complier

:: DOWNLOAD

 Sdiscover

:: MORE INFORMATION

Citation

Jason T. L. Wang, Thomas G. Marr, Dennis Shasha, Bruce A. Shapiro and Gung-Wei Chirn,
“Discovering Active Motifs in Sets of Related Protein Sequences and Using Them for Classification,”
Nucleic Acids Research, Vol. 22, No. 14, Aug. 1994, pp. 2769-2775.