CpGProD – Predict Mammalian Promoters Associated with CpG Islands

CpGProD

:: DESCRIPTION

CpGProD (CpG Island Promoter Detection) is an application for identifying mammalian promoter regions associated with CpG islands in large genomic sequences. Although it is strictly dedicated to this particular promoter class corresponding to ≈50% of the genes, CpGProD exhibits a higher sensitivity and specificity than other tools used for promoter prediction. Notably, CpGProD uses different parameters according to species (human, mouse) studied. Moreover, CpGProD predicts the promoter orientation on the DNA strand.

CpGProD Online Version

::DEVELOPER

PRABI-Doua

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows /  Mac OsX / Linux

:: DOWNLOAD

 CpGProD

:: MORE INFORMATION

Citation

Ponger, L. and Mouchiroud, D. (2001)
CpGProD: identifying CpG islands associated with transcription start sites in large genomic mammalian sequences.
Bioinformatics, 18, 631-633

MirCompare – Algorithm to Compare Plant and Mammalian miRNAs

MirCompare

:: DESCRIPTION

MirCompare is an innovative algorithm developed to compare sets of microRNAs belonging to different kingdoms, for their capacity to bind host mRNAs.

::DEVELOPER

MirCompare team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation:

Bioinformatics Prediction and Experimental Validation of MicroRNAs Involved in Cross-Kingdom Interaction.
Pirrò S, Minutolo A, Galgani A, Potestà M, Colizzi V, Montesano C.
J Comput Biol. 2016 Jul 18.

RamseyHAc 2010 – Prediction of Mammalian Transcription Factor Binding Sites

RamseyHAc 2010

:: DESCRIPTION

RamseyHAc (Histone acetylation) is a package of MATLAB M-files and data files is provided. The data files contain the feature tracks used for predicting TF binding sites, and the “ground truth” binding location data used to train the prediction model (both in MATLAB “.mat” file format). Also included is the file “GenomeRegions.bed” (in UCSC BED format) which describes the genome regions analyzed in this study. The M-files are the functions used to predict transcription factor binding, train the prediction model, and test the prediction model in a cross-validation framework.

::DEVELOPER

MAGNET project

:: REQUIREMENTS

 

  • Windows/Linux/MacOsX
  • MatLab

 

 RamseyHAc

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 1;26(17):2071-5. doi: 10.1093/bioinformatics/btq405. Epub 2010 Jul 27.
Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites.
Ramsey SA1, Knijnenburg TA, Kennedy KA, Zak DE, Gilchrist M, Gold ES, Johnson CD, Lampano AE, Litvak V, Navarro G, Stolyar T, Aderem A, Shmulevich I.

MamPhEA – Mammalian Phenotype Enrichment Analysis

MamPhEA

:: DESCRIPTION

MamPhEA is a web application dedicated to understanding functional properties of mammalian gene sets based on mouse-mutant phenotypes.

::DEVELOPER

MamPhEA team

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Sep 1;26(17):2212-3. doi: 10.1093/bioinformatics/btq359. Epub 2010 Jul 6.
MamPhEA: a web tool for mammalian phenotype enrichment analysis.
Weng MP1, Liao BY.

SVMicrO 20100315 – Mammalian MicroRNA Target Prediction

SVMicrO 20100315

:: DESCRIPTION

SVMicrO is a 2-stage SVM based new miRNA target prediction algorithm. It assumes a 2-stage structure including a site support vector machine (SVM) followed by a UTR-SVM. SMVicrO makes prediction based on 21 optimal site features and 18 optimal UTR features, selected by training from a comprehensive collection of 113 site and 30 UTR features.

::DEVELOPER

SVMicrO team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 SVMicrO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Sep 22;11:476. doi: 10.1186/1471-2105-11-476.
Improving performance of mammalian microRNA target prediction.
Liu H1, Yue D, Chen Y, Gao SJ, Huang Y.

GenemiR 1.0 – Unified Search of Mammalian microRNA Target Predictions

GenemiR 1.0

:: DESCRIPTION

The GenemiR software application is a tool aimed at biologists and bioinformaticians who wish to find prediction and expression patterns in sets of microRNAs and genes. The program works with mouse and human target prediction and expression data.

::DEVELOPER

Bertone Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 GenemiR

:: MORE INFORMATION