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.

PSEUDO 0.3.5 – Evaluate Empirical P-values for Linkage Scans

PSEUDO 0.3.5

:: DESCRIPTION

PSEUDO is a program for fast evaluation of empirical p-values for linkage scans. It can evaluate the significance of any Kong and Cox lod score and is extremely efficient when compared to standard methods for the evaluation of empirical p-values.

::DEVELOPER

Abecasis Lab

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Windows / Mac /  Linux

:: DOWNLOAD

PSEUDO

:: MORE INFORMATION

Citation:

Wigginton JE and Abecasis GR (2006).
An evaluation of the replicate pool method: quick estimation of genome-wide linkage peak p-values.
Genet Epidemiol 30:320-32

If you decide to use PSEUDO, please take a minute to register.

PlantMiRNAPred – Classification of Real and Pseudo Plant Pre-miRNAs

PlantMiRNAPred

:: DESCRIPTION

PlantMiRNAPred web server can be used to classify real plant pre-miRNAs and pseudo hairpins.

::DEVELOPER

NClab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Bioinformatics. 2011 May 15;27(10):1368-76. doi: 10.1093/bioinformatics/btr153. Epub 2011 Mar 26.
PlantMiRNAPred: efficient classification of real and pseudo plant pre-miRNAs.
Xuan P, Guo M, Liu X, Huang Y, Li W, Huang Y.

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.

PseKNC – Generating Pseudo K-tuple Nucleotide Composition

PseKNC

:: DESCRIPTION

The PseKNC (pseudo oligonucleotide composition, or pseudo K-tuple nucleotide composition), can be used to represent a DNA or RNA sequence with a discrete model or vector yet still keep considerable sequence order information, particularly the global or long-range sequence order information, via the physicochemical properties of its constituent oligonucleotides.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition.
Chen W, Lei TY, Jin DC, Lin H, Chou KC.
Anal Biochem. 2014 Jul 1;456:53-60. doi: 10.1016/j.ab.2014.04.001.

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.

PseKNC-General – Generating various modes of Pseudo Nucleotide Compositions

PseKNC-General

:: DESCRIPTION

PseKNC-General (the general form of pseudo k-tuple nucleotide composition) is a cross-platform standalone and open-source package that can be used to represent a DNA or RNA sequence with a discrete model or vector yet still keeping considerable sequence-order information, particularly the global or long-range sequence-order information via the physicochemical properties of its constituent oligonucleotides.

::DEVELOPER

LinDing Group

:: SCREENSHOTS

PseKNC-General

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 PseKNC-General

:: MORE INFORMATION

Citation

PseKNC-General: A cross-platform package for generating various modes of pseudo nucleotide compositions.
Chen W, Zhang X, Brooker J, Lin H, Zhang L, Chou KC.
Bioinformatics. 2015 Jan 1;31(1):119-20. doi: 10.1093/bioinformatics/btu602

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.

iMiRNA-PseDPC – microRNA Precursor Identification with a Pseudo Distance-pair Composition Approach

iMiRNA-PseDPC

:: DESCRIPTION

The web-server iMiRNA-PseDPC was developed for identifying the real microRNA precursors and false microRNA precursors.

::DEVELOPER

Liu Lab, Harbin Institute of Technology Shenzhen Graduate School.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

J Biomol Struct Dyn. 2015 Feb 3:1-28. [Epub ahead of print]
iMiRNA-PseDPC: microRNA precursor identification with a pseudo distance-pair composition approach.
Liu B1, Fang L, Liu F, Wang X, Chou KC.