Marina 1.03 – Identification of Over/under-represented TFBSs given large sets of Promoter-sequences

Marina 1.03

:: DESCRIPTION

Marina is an OS-independent GUI tool for computing TFBS abundance given two sets of promoter sequences. Marina performs such computations by harnessing 7 knowledge-discovery statistical metrics and the hypergeometric distribution so as to infer magnitude of TFBS over-representation. A standardization algorithm known as Iterative Proportional Fitting (IPF) enables “agreement” across these various metrics as to which TFBSs are the most over-represented and which are not.

::DEVELOPER

Parsa Hosseini

:: SCREENSHOTS

Marina

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 Marina

:: MORE INFORMATION

Citation

Plant Methods. 2013 Apr 11;9(1):12. doi: 10.1186/1746-4811-9-12.
Using an ensemble of statistical metrics to quantify large sets of plant transcription factor binding sites.
Hosseini P, Ovcharenko I, Matthews BF.

LASAGNA-Search 2.0 – Searching for Transcription Factor Binding Sites (TFBSs)

LASAGNA-Search 2.0

:: DESCRIPTION

LASAGNA-Search (Length-Aware Site Alignment Guided by Nucleotide Association) is an integrated webtool for transcription factor (TF) binding site search and visualization.

::DEVELOPER

LASAGNA-Search team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/MacOSX
  • Python

:: DOWNLOAD

 LASAGNA-Search

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 13.
LASAGNA-Search 2.0: integrated transcription factor binding site search and visualization in a browser.
Lee C, Huang CH.

TFBSs 1.0 – Predict Transcription Factor Binding Sites

TFBSs 1.0

:: DESCRIPTION

TFBSs is a web-servers for predicting transcription factor binding sites in the Saccharomyces cerevisiae genome.

::DEVELOPER

The Li’s Group of Theoretical Biophysics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Borowser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Guo-liang Fan and Qianzhong Li, Keli Yang,
TFBSs: a web server for Predicting transcription factor binding sites.
2012 IEEE International Conference on Cyber Technology in Automation, Control, and Intelligent Systems (CYBER), 2012,1:65-68.

TFBSs 1.0 – Predicting Transcription Factor Binding Sites

TFBSs 1.0

:: DESCRIPTION

TFBSs is a web server for Predicting transcription factor binding sites.

::DEVELOPER

The Li’s Group of Theoretical Biophysics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Borowser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Guo-liang Fan and Qianzhong Li, Keli Yang,
TFBSs: a web server for Predicting transcription factor binding sites.
2012 IEEE International Conference on Cyber Technology in Automation, Control, and Intelligent Systems (CYBER), 2012,1:65-68