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.

SWAN 0.3.0 – Statistical Structural Variation ANalyzer

SWAN 0.3.0

:: DESCRIPTION

SWAN is the first to introduce a statistically verifiable heterogeneity SV model to the community. As in SWAN, the genetic material sampled is no longer viewed as a homogenous mutant or reference sample but explicitly modeled as a mixture of both mutant and reference sequences with their fractions estimable.

::DEVELOPER

Ji Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • R

:: DOWNLOAD

SWAN

:: MORE INFORMATION

Citation

A genome-wide approach for detecting novel insertion-deletion variants of mid-range size.
LC Xia, S Sakshuwong, E Hopmans, J Bell, S Grimes, D Siegmund, H Ji, Nancy Zhang.
Nucleic Acids Research 44 (15), e126 (2016)