BPBAac – T3S effector prediction tool based on position-specific Amino Acid composition features in N-termini

BPBAac

:: DESCRIPTION

BPBAac, a classifier, was developed and trained using Support Vector Machine (SVM) based on the Aac feature extracted using a Bi-profile Bayes model.

::DEVELOPER

BioComputer, The Chinese University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/ Windows / MacOsX
R package

:: DOWNLOAD

BPBAac

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Mar 15;27(6):777-84. doi: 10.1093/bioinformatics/btr021. Epub 2011 Jan 13.
High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles.
Wang Y, Zhang Q, Sun MA, Guo D.

MDCinfer 1.0 – PPI Prediction tool based on Multiple Domain Cooperation analysis

MDCinfer 1.0

:: DESCRIPTION

MDCinfer aims to infer protein-protein interaction by considering cooperative domain interactions. Unlike most existing methods, it assumes cooperative-domain pairs but not only single-domain pairs as the basic units of a protein interaction. The interaction probabilities of single-domain pairs and cooperative-domain pairs are computed by a linear programming algorithm and a fast association probabilistic method. Novel protein interactions can be predicted by an extended probabilities model which can accommodate cooperative-domain pairs.

::DEVELOPER

APORC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows

:: DOWNLOAD

MDCinfer

:: MORE INFORMATION

Citation

Rui-Sheng Wang, Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang, and Luonan Chen.
Analysis on multi-domain cooperation for predicting protein-protein interactions.
BMC Bioinformatics, Vol. 8, 391, 2007.

PITA 6 – microRNA prediction tool

PITA 6

:: DESCRIPTION

PITA allows you to run the PITA algorithm on your choice of UTRs and microRNAs. PITA starts by scanning the UTR for potential microRNA targets (using the supplied seed matching tools) and then scores each site

::DEVELOPER

Segal Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / MacOsX / Linux
Perl

:: DOWNLOAD

PITA

:: MORE INFORMATION

Citation

Kertesz et al.,
The role of site accessibility in microRNA target recognition,
Nature Genetics 39, 1278 – 1284 (2007)

SpliceMachine – Splice Site Prediction Tool

SpliceMachine

:: DESCRIPTION

SpliceMachine is a splice site prediction tool that

shows state-of-the-art prediction performance on Arabidopsis thaliana and human sequences,
performs a computationally fast annotation and
can be trained by the user on its own data.

:: DEVELOPER

Bioinformatics & Systems Biology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

SpliceMachine

:: MORE INFORMATION

Citation:

Degroeve, S., Saeys, Y., De Baets, B., Rouzé, P., Van de Peer, Y. (2005)
Predicting splice sites from high-dimensional local context representations.
Bioinformatics 21, 1332-8.

ConStruct 3.2.5 – RNA Alignment Editor and Consensus Structure Prediction Tool

ConStruct 3.2.5

:: DESCRIPTION

ConStruct (construction of RNA consensus structures) is an RNA alignment editor and consensus structure prediction tool. It combines multiple sequence alignment, thermodynamic structure prediction and statistics in a semiautomatical fashion. Its sophisticated GUI guides the user through correcting an initial sequence alignment with respect to a consensus structure.

::DEVELOPER

Gerhard Steger <steger@biophys.uni-duesseldorf.de>,Heinrich-Heine-Universität Düsseldorf, Institut für Physikalische Biologie, Universitätsstr

:: SCREENSHOTS

:: REQUIREMENTS

Linux

:: DOWNLOAD

ConStruct

:: MORE INFORMATION

Citation:

Wilm, A., Linnenbrink, K. & Steger, G. (2008)
ConStruct: improved construction of RNA consensus structures.
BMC Bioinformatics 9, 219.