Tag: Composition

iNuc-PseKNC – Predicting Nucleosomes with Pseudo K-tuple Nucleotide Composition

iNuc-PseKNC

:: DESCRIPTION

The web-server iNuc-PseKNC was developed to predict nucleosome occupancy of H. sapiens, C. elegan and D. melanogaster

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iNuc-PseKNC: a sequence-based predictor for predicting nucleosome positioning in genomes with pseudo k-tuple nucleotide composition.
Guo SH, Deng EZ, Xu LQ, Ding H, Lin H, Chen W, Chou KC.
Bioinformatics. 2014 Jun 1;30(11):1522-9. doi: 10.1093/bioinformatics/btu083.

AodPred – Identifying Antioxidant Proteins by using optimal Dipeptide Compositions

AodPred

:: DESCRIPTION

The tool AodPred was developed to identify antioxidant proteins based on the sequence information.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Identifying Antioxidant Proteins by Using Optimal Dipeptide Compositions.
Feng P, Chen W, Lin H.
Interdiscip Sci. 2015 Sep 7.

VICMpred – Prediction of Functional Proteins of Gram-negative Bacteria using Amino Acid Patterns and Composition

VICMpred

:: DESCRIPTION

VICMpred aids in broad functional classification of bacterial proteins into virulence factors, information molecule, cellular process and metabolism molecule.

::DEVELOPER

VICMpred Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Saha, S. and Raghava, G.P.S. (2006)
VICMpred: SVM-based method for the prediction of functional proteins of gram-negative bacteria using amino acid patterns and composition.
Genomics Proteomics & Bioinformatics. 4(1):42-7

COPid – Composition Based Comprehensive Tool

COPid

:: DESCRIPTION

COPid is a web-server  to assist the researchers in annotating the function of a protein from its composition using whole or part of the protein.

::DEVELOPER

COPid team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

In Silico Biol. 2008;8(2):121-8.
COPid: composition based protein identification.
Kumar M1, Thakur V, Raghava GP.

BEBaC 20130425 – Estimate Bacterial Community Composition from 454 Sequencing data

BEBaC 20130425

:: DESCRIPTION

BEBaC (Bayesian Estimation of Bacterial Communities) is a software for estimating bacterial community composition from 454 sequencing data.

::DEVELOPER

Bayesian Statistics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 BEBaC

:: MORE INFORMATION

Citation:

Lu Cheng, Alan W. Walker and Jukka Corander
Bayesian estimation of bacterial community composition from 454 sequencing data
Nucl. Acids Res. (2012) 40 (12): 5240-5249.

BPBAac – T3S effector prediction tool based on position-specific Amino Acid composition features in N-termini

BPBAac

:: DESCRIPTION

BPBAac, a classifier, was developed and trained using Support Vector Machine (SVM) based on the Aac feature extracted using a Bi-profile Bayes model.

::DEVELOPER

BioComputer, The Chinese University of Hong Kong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows / MacOsX
  • R package

:: DOWNLOAD

 BPBAac

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Mar 15;27(6):777-84. doi: 10.1093/bioinformatics/btr021. Epub 2011 Jan 13.
High-accuracy prediction of bacterial type III secreted effectors based on position-specific amino acid composition profiles.
Wang Y, Zhang Q, Sun MA, Guo D.