CONCOCT 1.1.0 – Clustering cONtigs with COverage and ComposiTion

CONCOCT 1.1.0

:: DESCRIPTION

CONCOCT is a program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads.

::DEVELOPER

the Science for Life Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

CONCOCT

:: MORE INFORMATION

Citation

Alneberg J, Bjarnason BS, de Bruijn I, Schirmer M, Quick J, Ijaz UZ, Lahti L, Loman NJ, Andersson AF, Quince C.
Binning metagenomic contigs by coverage and composition.
Nat Methods. 2014 Nov;11(11):1144-6. doi: 10.1038/nmeth.3103. Epub 2014 Sep 14. PMID: 25218180.

SEK – Bacterial Community Composition

SEK

:: DESCRIPTION

SEK is a software for sparsity exploiting k-mer-based estimation of bacterial community composition.

::DEVELOPER

SEK team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX /Windows
  • MatLab

:: DOWNLOAD

  SEK

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 7. [Epub ahead of print]
SEK: Sparsity exploiting k-mer-based estimation of bacterial community composition.
Chatterjee S1, Koslicki D, Dong S, Innocenti N, Cheng L, Lan Y, Vehkaper? M, Skoglund M, Rasmussen LK, Aurell E, Corander J.

PLAAC – Prion-Like Amino Acid Composition

PLAAC

:: DESCRIPTION

PLAAC searches protein sequences to identify candidate prion subsequences using a hidden-Markov model (HMM) algorithm.

::DEVELOPER

Whitehead Institute for Biomedical Research

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 PLAAC

:: MORE INFORMATION

Citation

Bioinformatics. 2014 May 13. pii: btu310. [Epub ahead of print]
PLAAC: a web and command-line application to identify proteins with Prion-Like Amino Acid Composition.
Lancaster AK1, Nutter-Upham A1, Lindquist S2, King OD3.

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.

VirusSeeker – Virus Discovery and Virome Composition Analysis

VirusSeeker

:: DESCRIPTION

VirusSeeker is a set of fully automated and modular software package designed for mining next generation sequencing data form Illumina platform to identify sequences of viral origin.

::DEVELOPER

The Zhao Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

VirusSeeker

:: MORE INFORMATION

Citation:

Zhao G, Wu G, Lim ES, Droit L, Krishnamurthy S, Barouch DH, Virgin HW, Wang D.
VirusSeeker, a computational pipeline for virus discovery and virome composition analysis.
Virology. 2017 Mar;503:21-30. doi: 10.1016/j.virol.2017.01.005. Epub 2017 Jan 18. PMID: 28110145; PMCID: PMC5326578.

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.

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.