PredictSNP2 – Unified Platform for Prediction of SNP effect in Distinct Genomic Regions

PredictSNP2

:: DESCRIPTION

The PredictSNP is a consensus classifier combining six best performing prediction methods to provide more accurate and robust alternative to the predictions delivered by individual integrated tools.

PredictSNP2 extends the scope of genome analysis to the level of nucleotide substitutionsthat enables to identify disease­-related variants within the whole genome.

::DEVELOPER

Protein Engineering Group, Loschmidt Laboratories

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions.
Bendl J, Musil M, Štourač J, Zendulka J, Damborský J, Brezovský J.
PLoS Comput Biol. 2016 May 25;12(5):e1004962. doi: 10.1371/journal.pcbi.1004962.

PredictSNP: robust and accurate consensus classifier for prediction of disease-related mutations.
Bendl J, Stourac J, Salanda O, Pavelka A, Wieben ED, Zendulka J, Brezovsky J, Damborsky J.
PLoS Comput Biol. 2014 Jan;10(1):e1003440. doi: 10.1371/journal.pcbi.1003440

AMYLPRED – A Consensus Method for Amyloid Propensity Prediction

AMYLPRED

:: DESCRIPTION

AMYL-PRED is a consensus prediction method for identifying possible amyloidogenic regions in protein sequences.

::DEVELOPER

The Biophysics and Bioinformatics Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Struct Biol. 2009 Jul 9;9:44. doi: 10.1186/1472-6807-9-44.
Amyloidogenic determinants are usually not buried.
Frousios KK, Iconomidou VA, Karletidi CM, Hamodrakas SJ.

conSSert – Consensus Secondary Structure Prediction

conSSert

:: DESCRIPTION

conSSert is a SVM-based consenus secondary structure prediction method. Predictions from four popular secondary structure models (PSSpred, PSIPRED, Raptor-X, and SPINE-X) are integrated through the use of SVM models to produce highly accurate predictions, especially with regard to Q2-EH.

::DEVELOPER

the Multi-scale Systems Engineering Laboratory (MSEL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

conSSert: Consensus SVM model for accurate prediction of ordered secondary structure.
Kieslich CA, Smadbeck J, Khoury GA, Floudas C.
J Chem Inf Model. 2016 Feb 29.

MULCCH – MULti-task spectral Consensus Clustering for Hierarchically related tasks

MULCCH

:: DESCRIPTION

MULCCH is a consensus extension of a multi-task clustering algorithm to infer high-confidence strain-specific host response modules under infections from multiple virus strains.

::DEVELOPER

Roy Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MULCCH

:: MORE INFORMATION

Citation

Multi-task Consensus Clustering of Genome-wide Transcriptomes from Related Biological Conditions.
Niu Z, Chasman D, Eisfeld AJ, Kawaoka Y, Roy S.
Bioinformatics. 2016 Jan 21. pii: btw007.

Metassembler 1.5 – Combines multiple Whole Genome de novo Assemblies into a combined Consensus Assembly

Metassembler 1.5

:: DESCRIPTION

Metassembler is a software package for reconciling assemblies produced by de novo short-read assemblers such as SOAPdenovo and ALLPATHS-LG. The goal of assembly reconciliation, or “metassembly,” is to combine multiple assemblies into a single genome that is superior to all of its constituents

::DEVELOPER

Schatz Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Metassembler

:: MORE INFORMATION

Citation

Genome Biol. 2015 Sep 24;16:207. doi: 10.1186/s13059-015-0764-4.
Metassembler: merging and optimizing de novo genome assemblies.
Wences AH, Schatz MC

Consensus 20040414 – Web Interface for Finding DNA and Protein Patterns

Consensus 20040414

:: DESCRIPTION

Consensus Server determines consensus patterns in unaligned sequences. The algorithm is based on a matrix representation of a consensus pattern.

::DEVELOPER

Gerald Hertz (gzhertz AT alum.mit.edu), Stormo Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Consensus

:: MORE INFORMATION

Citation

Bioinformatics. 1999 Jul-Aug;15(7-8):563-77.
Identifying DNA and protein patterns with statistically significant alignments of multiple sequences.
Hertz GZ, Stormo GD.

Warpgroup 0.1.0 – Increased Precision of Metabolomic Data Processing by Consensus Integration Bound Analysis

Warpgroup 0.1.0

:: DESCRIPTION

Warpgroup is an R package for processing chromatography-mass spectrometry data.

::DEVELOPER

Patti Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / WIndows
  • R

:: DOWNLOAD

 Warpgroup

:: MORE INFORMATION

Citation:

Warpgroup: Increased Precision of Metabolomic Data Processing by Consensus Integration Bound Analysis.
Mahieu NG, Spalding J, Patti GJ.
Bioinformatics. 2015 Sep 30. pii: btv564.

CCTOP 1.00 – Constrained Consensus TOPology prediction server

CCTOP 1.00

:: DESCRIPTION

CCTOP server is a web-based application providing transmembrane topology prediction.

::DEVELOPER

CCTOP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

  CCTOP

:: MORE INFORMATION

Citation

CCTOP: a Consensus Constrained TOPology prediction web server.
Dobson L, Reményi I, Tusnády GE.
Nucleic Acids Res. 2015 May 5. pii: gkv451

CVhaplot – Consensus tool for Statistical Haplotyping

CVhaplot 2.01

:: DESCRIPTION

The CVhaplot packagea is small package of Perl scripts that implemented the consensus vote (CV) approach for nuclear haplotype reconstruction.

::DEVELOPER

Group of Molecular Ecology and Evolution, Institute of Zoology, Chinese Academy of Sciences

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX/ Windows
  • Perl

:: DOWNLOAD

 CVhaplot

:: MORE INFORMATION

Citation

Mol Ecol Resour. 2010 Nov;10(6):1066-70. doi: 10.1111/j.1755-0998.2010.02843.x.
CVhaplot: a consensus tool for statistical haplotyping.
Huang ZS1, Zhang DX.

proovread 2.12 – Large-scale high accuracy PacBio Correction through iterative Short Read Consensus.

proovread 2.12

:: DESCRIPTION

proovread is a hybrid correction pipeline for SMRT reads, which can be flexibly adapted on existing hardware and infrastructure from a laptop to a high performance computing cluster.

::DEVELOPER

Department of Bioinformatics, University of Würzburg,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux  / MacOsX
  • SHRiMP2
  • bash version 4 or above

:: DOWNLOAD

 proovread

 :: MORE INFORMATION

Citation:

proovread: large-scale high accuracy PacBio correction through iterative short read consensus.
Hackl T, Hedrich R, Schultz J, Förster F.
Bioinformatics. 2014 Jul 10. pii: btu392.