ComiR 20151020 – Combinatorial miRNA target prediction tool

ComiR 20151020

:: DESCRIPTION

ComiR (Combinatorial miRNA targeting) predicts whether a given mRNA is targeted by a set of miRNAs. ComiR uses miRNA expression to improve and combine multiple miRNA targets for each of the four prediction algorithms: miRanda, PITA, TargetScan and mirSVR.

::DEVELOPER

Benos Lab

 SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

C. Coronnello, R. Hartmaier, A. Arora, L. Huleihel, K.V. Pandit, A.S Bais, M. Butterworth, N. Kaminski, G.D. Stormo, S. Oesterreich, P.V. Benos (2012),
Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density,
PLoS Comput Bio 8(12): e1002830. doi:10.1371/journal.pcbi.1002830

snpEff 4.3T – Variant Annotation and Effect Prediction Tool

snpEff 4.3T

:: DESCRIPTION

snpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of variants on genes (such as amino acid changes).

SnpSift is a collection of tools to manipulate VCF (variant call format) files.

SnpEffWrapper takes a VCF and applies Annotations from a GFF using SnpEff

::DEVELOPER

snpEff team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

snpEff / SnpEffWrapper

:: MORE INFORMATION

Citation

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3.
Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, Land SJ, Lu X, Ruden DM.
Fly (Austin). 2012 Apr-Jun;6(2):80-92.

PlantPhos – Plant Phosphorylation Prediction Tool

PlantPhos

:: DESCRIPTION

PlantPhos is a web tool for predicting potential phosphorylation sites in plant proteins.

::DEVELOPER

CSB Laboratory 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PlantPhos: using maximal dependence decomposition to identify plant phosphorylation sites with substrate site specificity.
Lee TY, Bretaña NA, Lu CT.
BMC Bioinformatics. 2011 Jun 26;12:261. doi: 10.1186/1471-2105-12-261.

MBSTAR – microRNA Binding Site Prediction tool

MBSTAR

:: DESCRIPTION

MBSTAR (Multiple instance learning of Binding Sites of miRNA TARgets) is a web server for accurate prediction of true or functional miRNA binding sites.

::DEVELOPER

Bioinformatics Lab (MIU)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MBSTAR

:: MORE INFORMATION

Citation

Sci Rep. 2015 Jan 23;5:8004. doi: 10.1038/srep08004.
MBSTAR: multiple instance learning for predicting specific functional binding sites in microRNA targets.
Bandyopadhyay S, Ghosh D, Mitra R, Zhao Z

MycPermCheck 1.1 – Mycobacterium Tuberculosis Permeability Prediction tool for small Molecules

MycPermCheck 1.1

:: DESCRIPTION

MycPermCheck, given the current lack of precise molecular criteria determining mycobacterial permeability, represents an unprecedented prediction tool intended to support antimycobacterial drug discovery.

::DEVELOPER

the Research Group of Prof. Sotriffer

 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Merget et al. (2013)
MycPermCheck: The Mycobacterium tuberculosis permeability prediction tool for small molecules,
Bioinformatics, 29(1): 62-68.

IDP 0.1.8 – Gene Isoform Detection and Prediction tool

IDP 0.1.8

:: DESCRIPTION

IDP is an gene Isoform Detection and Prediction tool from Second Generation Sequencing and PacBio sequencing. It offers very reliable gene isoform identification with high sensitivity.

::DEVELOPER

Kin Fai Au

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOSX
  • Python

:: DOWNLOAD

 IDP

:: MORE INFORMATION

Citation

Kin Fai Au, Vittorio Sebastiano, Pegah Tootoonchi Afshar, Jens Durruthy Durruthy, Lawrence Lee, Brian A. Williams, Honoratus Van Bakel, Eric Schadt, Renee A. Reijo Pera, Jason Underwood, Wing Hung Wong
Characterization of the human ESC transcriptome by hybrid sequencing
Proc. Natl. Acad. Sci. USA 2013 110 (50) E4821-E4830

comTAR – Conserved Plant miRNA Target Prediction Tool

comTAR

:: DESCRIPTION

comTAR is a web tool for the prediction of miRNA targets that is mainly based on the conservation of the potential regulation in different species.

::DEVELOPER

IBR (Instituto de Biología Molecular y Celular de Rosario)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 Apr 12. [Epub ahead of print]
comTAR: a web tool for the prediction and characterization of conserved microRNA targets in plants.
Chorostecki U1, Palatnik JF.

miRPara 6.3 – SVM-based miRNA Prediction tool

miRPara 6.3

:: DESCRIPTION

miRPara predicts most probable mature miRNA coding regions from genome scale sequences in a species specific manner. We classified sequences from miRBase into animal, plant and overall categories and used a support vector machine (SVM) to train three models based on an initial set of 77 parameters related to the physical properties of the pre-miRNA and its miRNAs. By applying parameter filtering we found a subset of ~25 parameters produced higher prediction ability compared to the full set.

::DEVELOPER

The WIV Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 miRPara

:: MORE INFORMATION

Citation:

Wu Y., Wei B., Liu H., Li T., Rayner S.
MiRPara: a SVM-based software tool for prediction of most probable microRNA coding regions in genome scale sequences.
BMC Bioinformatics. 2011 Apr 19; 12(1):107

RSpred – Rifin/Stevor Prediction tool

RSpred

:: DESCRIPTION

RSpred based on a set of hidden Markov models and an evaluation program, automatically identifies STEVOR and RIFIN sequences as well as the sub-groups: A-RIFIN, B-RIFIN, B1-RIFIN and B2-RIFIN.

::DEVELOPER

IFM Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Genomics. 2011 Feb 18;12:119. doi: 10.1186/1471-2164-12-119.
RSpred, a set of Hidden Markov Models to detect and classify the RIFIN and STEVOR proteins of Plasmodium falciparum.
Joannin N, Kallberg Y, Wahlgren M, Persson B.

IGIPT – Integrated Genomic Island Prediction Tool

IGIPT

:: DESCRIPTION

IGIPT is a web-based integrated platform for the identification of genomic islands (GIs). It incorporates thirteen parametric measures based on anomalous nucleotide composition on a single platform, thus improving the predictive power of a horizontally acquired region, since it is known that no single measure can absolutely predict a horizontally transferred region.

::DEVELOPER

Dr.Nita ParekhRuchi Jain , Center for Computational Natural Sciences and Bioinformatics, International Institute of Information Technology – Hyderabad

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 IGIPT

:: MORE INFORMATION

Citation

IGIPT – Integrated genomic island prediction tool.
Jain R, Ramineni S, Parekh N.
Bioinformation. 2011;7(6):307-10. Epub 2011 Nov 20.