Tag: Motif Scanning

Swan v6 – Motif Scanning

Swan v6

:: DESCRIPTION

SWAN (Stubb With Another Null) is a software to meant for genome-wide prediction of regulatory targets of a motif using a Hidden Markov Model. It differs from Stubb in that instead of asking Does the sequence have more sites than expected from a random (background) model of sequences?, it asks the question Does the sequence have more sites than the average genome-wide frequency of sites?

::DEVELOPER

The Sinha Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Swan 

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2010 Jan 29;6(1):e1000652. doi: 10.1371/journal.pcbi.1000652.
Functional characterization of transcription factor motifs using cross-species comparison across large evolutionary distances.
Kim J, Cunningham R, James B, Wyder S, Gibson JD, Niehuis O, Zdobnov EM, Robertson HM, Robinson GE, Werren JH, Sinha S.

SADMAMA 20110410 – Motif Scanning and Detection of Significant Variation

SADMAMA 20110410

:: DESCRIPTION

SADMAMA (Significance Assessment of the Difference in MAtrix MAtches / SM) was originally designed to address the question of whether one set of sequences has more and/or better binding sites of a particular transcription factor than the other. The binding sites are modeled as matches to a, possibly gapped, position weight matrix (PWM) which is presumed to be known.

:: DEVELOPER

Uri Keich

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • C Compiler

:: DOWNLOAD

 SADMAMA

:: MORE INFORMATION

Citation:

Uri Keich et al.
Computational detection of significant variation in binding affinity across two sets of sequences with application to the analysis of replication origins in yeast
BMC Bioinformatics 2008, 9:372 doi:10.1186/1471-2105-9-372