PseAAC / PseAAC-Builder 3.0 / PseAAC-General – Generating Pseudo Amino Acid Composition

PseAAC / PseAAC-Builder 3.0 / PseAAC-General

:: DESCRIPTION

PseAAC is an algorithm that could convert a protein sequence into a digital vector that could be processed by pattern recognition algorithms. The design of PseAAC incorporated the sequence order information to improve the conventional amino acid compositions. The application of pseudo amino acid composition is very common, including almost every branch of computational proteomics.

PseAAC-Builder (PseAAC-General) is a cross-platform stand-alone program for generating various special Chou’s pseudo-amino acid compositions.

::DEVELOPER

PseAAC team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows with Cygwin

:: DOWNLOAD

 PseAAC-Builder 

:: MORE INFORMATION

Citation:

Hong-Bin Shen and Kuo-Chen Chou.
PseAAC: a flexible web-server for generating various kinds of protein pseudo amino acid composition.
Analytical Biochemistry, 2008, 373: 386-388.

Anal Biochem. 2012 Jun 15;425(2):117-9. doi: 10.1016/j.ab.2012.03.015. Epub 2012 Mar 27.
PseAAC-Builder: a cross-platform stand-alone program for generating various special Chou’s pseudo-amino acid compositions.
Du P1, Wang X, Xu C, Gao Y.

Pufeng Du, Shuwang Gu, Yasen Jiao.
PseAAC-General: Fast building various modes of general form of Chou’s pseudo-amino acid composition for large-scale protein datasets.
International Journal of Molecular Sciences 15 (2014) pp.3495-3506

PseAAC – Generating Pseudo Amino Acid Composition

PseAAC

:: DESCRIPTION

PseAAC is a web-server, by which users can generate various kinds of PseAA composition to best fit their need.

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PseAAC: a flexible web server for generating various kinds of protein pseudo amino acid composition.
Shen HB, Chou KC.
Anal Biochem. 2008 Feb 15;373(2):386-8. Epub 2007 Oct 13.

MBBC 1.1 – Metagenomic Binning Based on Composition

MBBC 1.1

:: DESCRIPTION

MBBC is a useful tool in metagenomic studies. It is a novel composition-based approach to bin environmental shotgun reads, by considering the k-mer frequency in reads and the inferred Markovian property of the unknown species or OTUs (operational taxonomic units).

::DEVELOPER

Hu Lab – Data Integration and Knowledge Discovery @ UCF

:: SCREENSHOTS

MBBC

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • Java

:: DOWNLOAD

 MBBC

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2015 Feb 5;16(1):36. [Epub ahead of print]
MBBC: an efficient approach for metagenomic binning based on clustering.
Wang Y, Hu H, Li X.

iRNA-Methyl / iRNA(m6A)-PseDNC – Identifying N6- methyladenosine sites

iRNA-Methyl /iRNA(m6A)-PseDNC

:: DESCRIPTION

The web-server iRNA-methyl was developed to identify the N6-methyladenosine (m6A). It was observed by the rigorous cross-validation test on the benchmark dataset that the accuracy achieved by the predictor in identifying m6A was 65.59%.

iRNA(m6A)-PseDNC was an updated version of iRNA-Methyl, which was developed to identify the N6-methyladenosine (m6A) in the Saccharomyces cerevisiae genome.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iRNA-Methyl: Identifying N(6)-methyladenosine sites using pseudo nucleotide composition.
Chen W, Feng P, Ding H, Lin H, Chou KC.
Anal Biochem. 2015 Dec 1;490:26-33. doi: 10.1016/j.ab.2015.08.021.

iRNA(m6A)-PseDNC: Identifying N6-methyladenosine sites using pseudo dinucleotide composition.
Chen W, Ding H, Zhou X, Lin H, Chou KC.
Anal Biochem. 2018 Nov 15;561-562:59-65. doi: 10.1016/j.ab.2018.09.002.

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.

PaPI – Pseudo Amino Acid Composition to Score human Protein-coding Variants

PaPI

:: DESCRIPTION

PaPI is a new machine-learning approach to classify and score human coding variants by estimating the probability to damage their protein-related function.

::DEVELOPER

laboratorio di Bioinformatica e Biologia Sintetica – Univ. of Pavia

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PaPI: pseudo amino acid composition to score human protein-coding variants.
Limongelli I, Marini S, Bellazzi R.
BMC Bioinformatics. 2015 Apr 19;16(1):123. doi: 10.1186/s12859-015-0554-8.

iDNA-Methyl – Identifying DNA Methylation Sites via Pseudo Trinucleotide Composition

iDNA-Methyl

:: DESCRIPTION

The web-server iDNA-Methyl is according to its genetic codes by combining its trinucleotide composition (TNC) and the pseudo amino acid components (PseAAC) of the protein translated from the DNA sample. And by means of the approach of optimizing training datasets for predicting DNA methylation sites. Rigorous cross-validations on a set of experiment-confirmed datasets have indicated that these new predictors remarkably outperformed their counterparts in the existing prediction methods

::DEVELOPER

JCI BioInfo Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iDNA-Methyl: Identifying DNA methylation sites via pseudo trinucleotide composition.
Liu Z, Xiao X, Qiu WR, Chou KC.
Anal Biochem. 2015 Jan 14. pii: S0003-2697(14)00569-7. doi: 10.1016/j.ab.2014.12.009.