RNAConSLOpt 1.2 – Predicting Consensus stable local optimal Structures for Aligned RNA Sequences

RNAConSLOpt 1.2

:: DESCRIPTION

RNAConSLOpt is a program for predicting consensus stable local optimal structures (represented by stack configurations) for aligned RNA sequences. RNAConSLOpt can be used to predict consensus alternate structures for riboswitches.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNAConSLOpt

:: MORE INFORMATION

Citation

Int J Bioinform Res Appl. 2014;10(4):498-518. doi: 10.1504/IJBRA.2014.062997.
Finding consensus stable local optimal structures for aligned RNA sequences and its application to discovering riboswitch elements.
Li Y, Zhong C, Zhang S.

RNAscf 1.1 – Consensus Folding of Unaligned RNA sequences

RNAscf 1.1

:: DESCRIPTION

RNAscf is a program for RNA consensus folding for a set of unaligned RNA sequences.

::DEVELOPER

UCF Computational Biology and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

 RNAscf

:: MORE INFORMATION

Citation

J Comput Biol. 2006 Mar;13(2):283-95.
Consensus folding of unaligned RNA sequences revisited.
Bafna V, Tang H, Zhang S.

RadCon 1.1.6 – Phylogenetic Tree Consensus & Comparison Program

RadCon 1.1.6

:: DESCRIPTION

RadCon is a phylogenetic tree consensus and comparison program for Macs (OS 7.5 – 9).Implemented methods include the strict reduced consensus method, leaf stability, cladistic information content, double decay analysis and matrix representation with parsimony.

::DEVELOPER

RadCon team

:: SCREENSHOTS

:: REQUIREMENTS

  • Mac(OS 7.5 – 9)

:: DOWNLOAD

 RadCon

:: MORE INFORMATION

Citation

Joseph L. Thorley and Roderic D. M. Page
RadCon: phylogenetic tree comparison and consensus
Bioinformatics (2000) 16 (5): 486-487.

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

Stormo Lab

:: 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.

SSCon – Consensus-based Secondary Structure predictor

SSCon

:: DESCRIPTION

SScon is a first-of-its-kind comprehensive design of a SS consensus predictor which considers 12 modern standalone SS predictors and utilize Support Vector Machine (SVM) to combine their predictions.

::DEVELOPER

Kurgan Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux/ MacOsX
  • Java

:: DOWNLOAD

  SSCon

 :: MORE INFORMATION

Citation

J Biomol Struct Dyn. 2014;32(1):36-51. doi: 10.1080/07391102.2012.746945. Epub 2013 Jan 9.
Comprehensively designed consensus of standalone secondary structure predictors improves Q3 by over 3%.
Yan J1, Marcus M, Kurgan L.

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.

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.

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