Tag: Prediction

JPOP 0.1 – Prediction of Operon Structures

JPOP 0.1

:: DESCRIPTION

JPOP (Joint Prediction of Operons)is a set java programs and Mathlab scripts to aid in the prediction of operon structures. JPOP integrates three sources of genomic information to predict operon structures in a sequenced genome:
1) COG (cluster of orthologs) assignments;
2) Phylogenetic profiles of genes;
3) Intergenic distances between gene pairs.

::DEVELOPER

the Computational Systems Biology Laboratory at the University of Georgia 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 JPOP 

:: MORE INFORMATION

Citation

Xin Chen, Zhengchang Su, Ying Xu and Tao Jiang.
Computational prediction of operons in Synechococcus sp. WH8102.
Gemone Informatics 15: 211-222, 2004

Cubic 2.0.4 / JCubic 1.1 – Protein Binding Site Prediction

Cubic 2.0.4 / JCubic 1.1

:: DESCRIPTION

Cubic is a tool to be used for protein binding site prediction.

JCUBIC is a Java-based GUI for CUBIC program which can be used for transcription factor binding site prediction.

::DEVELOPER

the Computational Systems Biology Laboratory at the University of Georgia 

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 Cubic / JCubic

:: MORE INFORMATION

Citation

Victor Olman, Jizhu Lu, PhuongAn Dam, Zhengchang Su, Ying Xu.
CUBIC: Search for Binding Sites.
CSB 2004: 666-667

Musite 1.0.1 – Prediction of Both General and Kinase-specific Protein Phosphorylation Sites

Musite 1.0.1

:: DESCRIPTION

Musite is a Java-based standalone application for predicting both general and kinase-specific protein phosphorylation sites. Musite pre-trained prediction models for 6 eukaryotic organisms: Homo sapiens, Mus musculus, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, and Arabidopsis thaliana. It is advisable to train your own prediction models from your specific training data, using the customized model training tool in Musite.

::DEVELOPER

Digital Biology Laboratory

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 Musite

:: MORE INFORMATION

Citation

Jianjiong Gao, Jay J. Thelen, A. Keith Dunker, and Dong Xu.
Musite, a Tool for Global Prediction of General and Kinase-Specific Phosphorylation Sites.
Molecular & Cellular Proteomics. 2010. 9(12):2586-600.

MUPRED – Protein Secondary Structure Prediction

MUPRED

:: DESCRIPTION

MUPRED is a protein secondary structure and solvent accessibility prediction server based on a novel framework

MUPRED Online version

:DEVELOPER

Digital Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Web Server

:: DOWNLOAD

 MUPRED

:: MORE INFORMATION

Citation

Bondugula R, Xu D.
MUPRED: a tool for bridging the gap between template based methods and sequence profile based methods for protein secondary structure prediction.
Proteins. 2007 Feb 15;66(3):664-70.

GeneFAS – Gene Function Prediction

GeneFAS

:: DESCRIPTION

GeneFAS (Gene Function Annotation System) is a java based graphical user interface for prediction of gene function using multiple sources of data.

::DEVELOPER

Digital Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Java

:: DOWNLOAD

 GeneFAS

:: MORE INFORMATION

Citation

Joshi T, Zhang C, Lin GN, Song Z, Xu D.
GeneFAS: A tool for prediction of gene function using multiple sources of data.
Methods Mol Biol. 2008;439:369-86.

FunSiP 0.8.1b – Prediction of Functional Sites in DNA

FunSiP 0.8.1b

:: DESCRIPTION

FunSiP : A Modular and Extensible Classifier for the Prediction of Functional Sites in DNA. FunSip is a platform that uses a very general approach towards the classification of functional sites in DNA sequences. The program uses an ab initio approach towards the identification of these sites, and extends SpliceMachine, a previously developed splice site predictor that shows state-of-the-art performance for both donor and acceptor splice site recognition in the human and Arabidopsis thaliana genome.

::DEVELOPER

Bioinformatics & Systems Biology

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/windows/MacOsX
  • Java

:: DOWNLOAD

 FunSiP

:: MORE INFORMATION

Citation:

Van Bel, M., Saeys, Y., Van de Peer, Y. (2008)
FunSiP : A Modular and Extensible Classifier for the Prediction of Functional Sites in DNA.
Bioinformatics 24, 1532-3.

Orb 1.2 / orbplus 1.1.2 – Chemical Shift Prediction

Orb 1.2

:: DESCRIPTION

orb predicts chemical shifts based on homologous proteins employing a graphical user interface. Orb thoughtfully considers global sequence homology, local sequence homology, structural homology, and molecular homology in determining its predictions.

orbplus is a structural Feature Prediction Tool – This software summarizes and predicts the properties of an input protein using only the assigned chemical shift information of a target protein.

::DEVELOPER

Brian Sykes Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 Orb , orbplus

:: MORE INFORMATION

Citation

 

Wolfram Gronwald , R. Boyko, Frank Sonnichsen , David Wishart , and B.D. Sykes .
ORB, a homology-based program for the prediction of protein NMR chemical shifts
J.Biomol.10, 165-181(1997)

Twinscan/N-SCAN 4.1.2 – Gene Structure Prediction

Twinscan/N-SCAN 4.1.2

:: DESCRIPTION

Twinscan/N-SCAN is a suite of software for gene-structure prediction. Twinscan is currently available for Mammals, Caenorhabditis (worm), Dicot plants, and Cryptococci. N-SCAN is available for human and Drosophila (fruitfly).

::DEVELOPER

The Brent Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

   Twinscan

:: MORE INFORMATION

Citation

Flicek P, Keibler E, Hu P, Korf I, Brent MR.
Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map.
Genome Res. 2003 Jan;13(1):46-54.

Kinwalker – Algorithm for Prediction of RNA Folding Trajectories

Kinwalker

:: DESCRIPTION

The  Kinwalker  algorithm performs cotranscriptional folding of RNAs, starting at a user a specified structure (default: open chain) and ending at the minimum free energy structure. Folding events are performed between transcription of additional bases and are regulated by barrier heights between the source and target structure.

::DEVELOPER

Bioinformatics Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  Kinwalker

:: MORE INFORMATION

Citation

J Mol Biol. 2008 May 23;379(1):160-73. Epub 2008 Mar 6.
Folding kinetics of large RNAs.
Geis M, Flamm C, Wolfinger MT, Tanzer A, Hofacker IL, Middendorf M, Mandl C, Stadler PF, Thurner C.

AveRNA – Ensemble-based Prediction of RNA Secondary Structures.

AveRNA

:: DESCRIPTION

The AveRNA program predicts secondary structures by combining structures obtained from 11 other prediction programs.

AveRNA Online Version

::DEVELOPER

BETA LAB – University of British Columbia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 AveRNA

:: MORE INFORMATION

Citation:

Nima Aghaeepour and Holger Hoos:
Ensemble-based Prediction of RNA Secondary Structures.
RNA, submitted for publication, May 2011.

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