TEPITOPEpan – A pan-specific method for Peptide:MHCII Binding Prediction

TEPITOPEpan

:: DESCRIPTION

TEPITOPEpan extends the original TEPITOPE method to peptide binding prediction to more alleles.

::DEVELOPER

Laboratory of Data Mining and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2012;7(2):e30483. doi: 10.1371/journal.pone.0030483. Epub 2012 Feb 23.
TEPITOPEpan: extending TEPITOPE for peptide binding prediction covering over 700 HLA-DR molecules.
Zhang L1, Chen Y, Wong HS, Zhou S, Mamitsuka H, Zhu S.

ProbTF – Transcription Factor Binding Prediction from multiple data sources

ProbTF

:: DESCRIPTION

ProbTF provides a flexible and principled probabilistic framework to predict transcription factor binding from multiple data sources. ProbTF uses the standard position specific frequency matrix (PSFM) and the d:th order Markovian background models as its building blocks (this choice is arbitrary though, and similar methods can be implemented using other models as well). In addition, ProbTF can incorporate basically any genome-level information (i.e., information at the level of individual nucleotides) in a probabilistic manner to estimate binding probabilities.

::DEVELOPER

Prof. (pro term) Harri Lähdesmäki, D.Sc. (Tech)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX / Windows
  • Matlab

:: DOWNLOAD

 ProbTF

:: MORE INFORMATION

Citation:

Harri Lähdesmäki, Alistair G. Rust and Ilya Shmulevich,
Probabilistic inference of transcription factor binding from multiple data sources,
PLoS ONE, Vol. 3, No. 3, e1820, 2008.