MobiDB-lite 3.8.4 – Long Disorder Consensus Predictor

MobiDB-lite 3.8.4

:: DESCRIPTION

MobiDB-lite is an optimized method for highly specific predictions of long intrinsically disordered regions (IDRs). The method uses 8 different predictors to derive a consensus which is filtered for spurious short predictions in a second step.

::DEVELOPER

The BioComputing UP lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Java

:: DOWNLOAD

MobiDB-lite

:: MORE INFORMATION

Citation:

Necci M, Piovesan D, Clementel D, Dosztányi Z, Tosatto SCE.
MobiDB-lite 3.0: fast consensus annotation of intrinsic disorder flavours in proteins.
Bioinformatics. 2020 Dec 16:btaa1045. doi: 10.1093/bioinformatics/btaa1045. Epub ahead of print. PMID: 33325498.

ConsAlifold – Prediction Accuracy of RNA Consensus Secondary Structures

ConsAlifold

:: DESCRIPTION

ConsAlifold is a dynamic programming-based method that predicts the consensus secondary structure of an RNA sequence alignment.

::DEVELOPER

ConsAlifold team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
Python

:: DOWNLOAD

ConsAlifold

:: MORE INFORMATION

Citation

Tagashira M, Asai K.
ConsAlifold: Considering RNA Structural Alignments Improves Prediction Accuracy of RNA Consensus Secondary Structures.
Bioinformatics. 2021 Oct 25:btab738. doi: 10.1093/bioinformatics/btab738. Epub ahead of print. PMID: 34694364.

EPCES – Prediction of Antigenic Epitopes on Protein Surfaces by Consensus Scoring

EPCES

:: DESCRIPTION

EPCES (Epitopes ConsEnsus Scoring) is a new antigen Epitope Prediction method from six different scoring functions – residue epitope propensity, conservation score, side-chain energy score, contact number, surface planarity score, and secondary structure composition.

::DEVELOPER

System Biology Laboratory Of Chi Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2009 Sep 22;10:302. doi: 10.1186/1471-2105-10-302.
Prediction of antigenic epitopes on protein surfaces by consensus scoring.
Liang S1, Zheng D, Zhang C, Zacharias M.

CABS-fold – Server for de novo and Consensus-based prediction of Protein Structure

CABS-fold

:: DESCRIPTION

CABS-fold is a server that provides tools for protein structure prediction from sequence only (de novo modeling) and also using alternative templates (consensus modeling).

::DEVELOPER

Laboratory of Theory of Biopolymers, University of Warsaw

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web Browser

:: DOWNLOAD

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W406-11. doi: 10.1093/nar/gkt462. Epub 2013 Jun 8.
CABS-fold: Server for the de novo and consensus-based prediction of protein structure.
Blaszczyk M1, Jamroz M, Kmiecik S, Kolinski A.

MAPSCI 1.0 – Multiple Alignment of Protein Structures and Consensus Identification

MAPSCI 1.0

:: DESCRIPTION

MAPSCI is an algorithm to compute a multiple structure alignment for a set of proteins and to generate a consensus structure.

::DEVELOPER

MAPSCI team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows
C++ Compiler

:: DOWNLOAD

MAPSCI

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Feb 2;11:71. doi: 10.1186/1471-2105-11-71.
Multiple structure alignment and consensus identification for proteins.
Ilinkin I1, Ye J, Janardan R.

proovread 2.14.1 – Large-scale high accuracy PacBio Correction through iterative Short Read Consensus.

proovread 2.14.1

:: 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.

CVhaplot 2.01 – 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

The State Key Laboratory of Integrated Pest Management

:: 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.

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

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

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.