MAIRA 0.1.7 – Real-time Taxonomic and Functional analysis of long Reads on a laptop

MAIRA 0.1.7

:: DESCRIPTION

MAIRA is a new standalone program for interactive taxonomic and functional analysis of long read metagenomic sequencing data on a laptop without internet access. The program performs fast, online, genus-level analysis, and on-demand, detailed taxonomic and functional analysis. It uses two levels of frame-shift-aware alignment of DNA reads against protein reference sequences, and then performs detailed analysis using a protein synteny graph.

::DEVELOPER

the Algorithms in Bioinformatics lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows

:: DOWNLOAD

MAIRA

:: MORE INFORMATION

Citation

Albrecht B, Bağcı C, Huson DH.
MAIRA- real-time taxonomic and functional analysis of long reads on a laptop.
BMC Bioinformatics. 2020 Sep 17;21(Suppl 13):390. doi: 10.1186/s12859-020-03684-2. PMID: 32938391; PMCID: PMC7495841.

ENNB – Feature Selection and Comparison in Functional Analysis of Metagenomes

ENNB

:: DESCRIPTION

ENNB is a two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes.In the first stage of the proposed procedure, the informative features are selected using Elastic Net as reducing the dimension of metagenomic data; in the second stage the differentially abundant features are detected using generalized linear models with a Negative Binomial distribution.

::DEVELOPER

Lingling An

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
R

:: DOWNLOAD

ENNB

:: MORE INFORMATION

Citation

A two-stage statistical procedure for feature selection and comparison in functional analysis of metagenomes.
Pookhao N, Sohn M, Li Q, Jenkins I, Du R, Jiang H, An L.
Bioinformatics. 2014 Sep 24. pii: btu635.

FunNet 1.00-3 – Functional Analysis of Transcriptional Networks

FunNet 1.00-3

:: DESCRIPTION

“FunNet” is an integrative tool for analyzing gene co-expression networks from microarray expression data. The analytic model implemented in this library involves two abstraction layers: transcriptional and functional (biological roles). A functional profiling technique using Gene Ontology and KEGG annotations is applied to extract a list of relevant biological themes from microarray expression profiling data.

::DEVELOPER

Corneliu Henegar

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
R package

:: DOWNLOAD

FunNet

:: MORE INFORMATION

Citation

FunNet: an integrative tool for exploring transcriptional interactions
Prifti E, Zucker JD, Clément K and Henegar C.
Bioinformatics 2008, doi: 10.1093/bioinformatics/btn492.

GOfact 20051017 – An Integrated Strategy for Functional Analysis in Large-scale Proteomic Research by Gene Ontology

GOfact 20051017

:: DESCRIPTION

GOfact is developed to identify the functional distribution and the significantly enriched functional categories of the proteomic expression profile. It would be helpful for understanding the overall functions of these identified proteins and supply the fundamental information for further bioinformatics exploration.

::DEVELOPER

Li Dong

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux/Windows
Perl

:: DOWNLOAD

GOfact

:: MORE INFORMATION

Citation

Li Dong, Li Jian-Qi, Ouyang Shu-Guang, Wang Jian, Xu Xiaojie, Zhu Yun-Ping, He Fu-Chu.
An Integrated Strategy for Functional Analysis in Large-scale Proteomic Research by Gene Ontology.
Biochemistry and Biophysics 2005,32(11):1026-1029

GOplot 1.0.2 – Visualization Of Functional Analysis Data

GOplot 1.0.2

:: DESCRIPTION

GOplot is an R package for implementation of multilayered visualizations for enhanced graphical representation of functional analysis data.

::DEVELOPER

Wencke Walter <wencke.walter at arcor.de>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows/ MacOsX
R

:: DOWNLOAD

GOplot

:: MORE INFORMATION

Citation

GOplot: an R package for visually combining expression data with functional analysis.
Walter W, Sánchez-Cabo F, Ricote M.
Bioinformatics. 2015 May 11. pii: btv300

A-DaGO-Fun / DaGO-Fun – Gene Ontology Semantic Similarity based Functional Analysis

A-DaGO-Fun / DaGO-Fun

:: DESCRIPTION

A-DaGO-Fun is a python library that provides a comprehensive and customized set of Gene Ontology (GO) based functional analysis tools that exploit the biological knowledge that GO offers in describing genes or groups of genes through the use of GO semantic similarity measures for biological knowledge discovery.

The DaGO-Fun tool is a an integrated set of GO-based functional analysis tools incorporating the large amounts of biological knowledge that GO offers in describing genes or groups of genes.

::DEVELOPER

The UCT Computational Biology Group (CBIO)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

A-DaGO-Fun: An adaptable Gene Ontology semantic similarity based functional analysis tool.
Mazandu GK, Chimusa ER, Mbiyavanga M, Mulder NJ.
Bioinformatics. 2015 Oct 17. pii: btv590.

DaGO-Fun: tool for Gene Ontology-based functional analysis using term information content measures.
Mazandu GK, Mulder NJ.
BMC Bioinformatics. 2013 Sep 25;14:284. doi: 10.1186/1471-2105-14-284.

SUPER-FOCUS 0.34 – Agile Functional Analysis of Shotgun Metagenomic data

SUPER-FOCUS 0.34

:: DESCRIPTION

SUPER-FOCUS (SUbsystems Profile by databasE Reduction using FOCUS) an agile homology-based approach using a reduced SEED database to report the subsystems present in metagenomic samples and profile their abundances.

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Mac OsX / Linux
Python

:: DOWNLOAD

SUPER-FOCUS

:: MORE INFORMATION

Citation:

SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data.
Silva GG, Green KT, Dutilh BE, Edwards RA.
Bioinformatics. 2015 Oct 9. pii: btv584.

Mashup – Compact Integration of Multi-Network Topology for Functional Analysis of Genes

Mashup

:: DESCRIPTION

Mashup is a framework for compact integration of multi-network topology for functional analysis of genes.

::DEVELOPER

Bonnie Berger

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / Windows / MacOsX
MatLab

:: DOWNLOAD

Mashup

:: MORE INFORMATION

Citation:

Compact Integration of Multi-Network Topology for Functional Analysis of Genes
Hyunghoon Cho, Bonnie Berger, Jian Peng
Cell Systems 3 (6), 2016

miR2GO – Comparative Functional analysis for microRNAs

miR2GO

:: DESCRIPTION

miR2GO is a web based platform for comparative analyses of human miRNA functions. It includes two programs: miRmut2GO (Functional analysis of genetic and somatic mutations in microRNAs) and miRpair2GO (Comparative functional analysis for microRNA pairs).

::DEVELOPER

Yan Cui’s Lab at University of Tennessee Health Science Center

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

miR2GO: Comparative functional analysis for microRNAs.
Bhattacharya A, Cui Y.
Bioinformatics. 2015 Mar 10. pii: btv140.

Biowine – Knowledge base for Vitis vinifera Functional analysis

Biowine

:: DESCRIPTION

Biowine is a knowledge base of genomic data of Vitis-vinifera, containing NGS data from several samples of grapevine.

::DEVELOPER

Biowine team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Web browser

:: DOWNLOAD

:: MORE INFORMATION

Citation:

BMC Syst Biol. 2015;9 Suppl 3:S5. doi: 10.1186/1752-0509-9-S3-S5. .
A knowledge base for Vitis vinifera functional analysis.
Pulvirenti A, Giugno R, Distefano R, Pigola G, Mongiovi M, Giudice G, Vendramin V, Lombardo A, Cattonaro F, Ferro A.