iEsGene-ZCPseKNC – Identify eseential Genes based on Z curve pseudo k-tuple nucleotide composition

iEsGene-ZCPseKNC

:: DESCRIPTION

iEsGene-ZCPseKNC is a webserver which can identify essential gene for archaea.

::DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Chen J, et al.
iEsGene-ZCPseKNC: identify archaea essential genes based on Z curve pseudo k-tuple nucleotide composition,
IEEE ACCESS 
2019; 7:165241-165247.

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

:: 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.

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

Xiao 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.

iRSpot-TNCPseAAC – Identify Recombination Spots with Trinucleotide Composition and Pseudo Amino Scid Components

iRSpot-TNCPseAAC

:: DESCRIPTION

The web-server iRSpot-TNCPseAAC was developed for identifying the recombination hotspots and coldspots.

::DEVELOPER

Xiao Lab

:: SCREENSHOTS

n/a

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

iRSpot-TNCPseAAC: identify recombination spots with trinucleotide composition and pseudo amino acid components.
Qiu WR, Xiao X, Chou KC.
Int J Mol Sci. 2014 Jan 24;15(2):1746-66. doi: 10.3390/ijms15021746.

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.

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.

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