Panache v1.0.0 – PANgenome Analyzer with CHromosomal Exploration

Panache v1.0.0

:: DESCRIPTION

Panache is a web-based interface designed for the visualization of linearized pangenomes. It can be used to show presence/absence information of pangenomic blocks of sequence or genes in a browser-like display.

::DEVELOPER

Panache team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser
:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Durant É, Sabot F, Conte M, Rouard M.
Panache: a Web Browser-Based Viewer for Linearized Pangenomes.
Bioinformatics. 2021 Oct 2:btab688. doi: 10.1093/bioinformatics/btab688. Epub ahead of print. PMID: 34601567.

PDA 20060711 – Pooled DNA Analyzer

PDA 20060711

:: DESCRIPTION

PDA ( Pooled DNA analyzer ) is a powerful tool for analyses of pooled DNA data.

::DEVELOPER

Hsin-Chou Yang and Cathy SJ Fann(Institute of Biomedical Sciences, Academia Sinica, Taiwan)

:: SCREENSHOTS

::REQUIREMENTS

:: DOWNLOAD

 PDA

:: MORE INFORMATION

Citation

Hsin-Chou Yang, Chia-Ching Pan, Chin-Yu Lin and Cathy SJ Fann (2006).
PDA: pooled DNA analyzer.
BMC Bioinformatics, 7: 233.

BiNA 2.4.1.1 – Biological Network Analyzer

BiNA 2.4.1.1

:: DESCRIPTION

BiNA is a workbench for visualizing and analyzing biological networks. Various biological networks can be displayed, edited and analyzed.

::DEVELOPER

BiNA team

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

 BiNA

:: MORE INFORMATION

Citation:

BiNA: a visual analytics tool for biological network data.
Gerasch A, Faber D, Küntzer J, Niermann P, Kohlbacher O, Lenhof HP, Kaufmann M.
PLoS One. 2014 Feb 13;9(2):e87397. doi: 10.1371/journal.pone.0087397.

GREAM – Genomic Repeat Element Analyzer for Mammals

GREAM

:: DESCRIPTION

GREAM allows to analyze the distribution of repeat elements in the gene neighborhood region of seventeen mammalian species (such as Human, Mouse, Rat, Dog, Monkey, Gorilla, Gibbon, Cow, Marmoset, Opposum, Platypus, Elephant, Orangutan, Rabbit, Horse, Pig and Chimpanzee).

::DEVELOPER

Institute of Bioinformatics and Applied Biotechnology, Bangalore, India,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Server
  • Perl

:: DOWNLOAD

GREAM

:: MORE INFORMATION

Citation

Chandrashekar DS, Dey P, Acharya KK.
GREAM: A Web Server to Short-List Potentially Important Genomic Repeat Elements Based on Over-/Under-Representation in Specific Chromosomal Locations, Such as the Gene Neighborhoods, within or across 17 Mammalian Species.
PLoS One. 2015 Jul 24;10(7):e0133647. doi: 10.1371/journal.pone.0133647. PMID: 26208093; PMCID: PMC4514817.

ChiRA 1.4.3 – Chimeric Read Analyzer

ChiRA 1.4.3

:: DESCRIPTION

ChiRA is a set of tools to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH etc.

::DEVELOPER

Pavankumar Videm @ Bioinformatics Group Albert-Ludwigs-University Freiburg

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

ChiRA

:: MORE INFORMATION

Citation

Videm P, Kumar A, Zharkov O, Grüning BA, Backofen R.
ChiRA: an integrated framework for chimeric read analysis from RNA-RNA interactome and RNA structurome data.
Gigascience. 2021 Jan 29;10(2):giaa158. doi: 10.1093/gigascience/giaa158. PMID: 33511995; PMCID: PMC7844879.

Tea 0.6.2 – Transposable Element Analyzer

Tea 0.6.2

:: DESCRIPTION

Tea is a tool for detection of retrotransposition events in whole-genome sequencing data.

::DEVELOPER

Peter Park’s lab at CBMI, Harvard Medical School

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Tea

:: MORE INFORMATION

Citation

Eunjung Lee et al.
Landscape of Somatic Retrotransposition in Human Cancers
Science 24 August 2012: Vol. 337 no. 6097 pp. 967-971

Sadic / ProCoCoA 1.1b10 – Simple Atom Depth Index Calculator / Protein Core Composition Analyzer

Sadic / ProCoCoA 1.1b10

:: DESCRIPTION

Sadic/ProCoCoA is able to calculate the atom depth value for every atom of a protein structure, giving a lot of intrinsic information of 3D composition of the macromolecule and its core.

::DEVELOPER

SBL (Stuctural Biology Laboratory), University of Siena

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation:

Comput Biol Chem. 2013 Apr;43:29-34. doi: 10.1016/j.compbiolchem.2012.12.007. Epub 2012 Dec 31.
ProCoCoA: A quantitative approach for analyzing protein core composition.
Bottini S1, Bernini A, De Chiara M, Garlaschelli D, Spiga O, Dioguardi M, Vannuccini E, Tramontano A, Niccolai N.

Gelapp 1.2.7 – DNA & Prot Gel Analyzer

Gelapp 1.2.7

:: DESCRIPTION

Gelapp is an app that allows you to analyze gel (both agarose and PAGE) bands with a log graph automatically generated from the markers. It allows automatic detection and loading for future uses. Utilizing Gabor filter, this app allows users to improve detection of bands automatically. For poor quality images, users can click can manually draw a box on the desired band or click on the image to determine the specified location.

::DEVELOPER

Antibody & Product Development Team of BII-p53Lab ASTAR

:: SCREENSHOTS

:: REQUIREMENTS

  • iOS / Android

:: DOWNLOAD

Gelapp for iOS / for Android.

:: MORE INFORMATION

Citation

Nguyen PV, Ghezal A, Hsueh YC, Boudier T, Gan SK, Lee HK.
Optimal processing for gel electrophoresis images: Applying Monte Carlo Tree Search in GelApp.
Electrophoresis. 2016 Aug;37(15-16):2208-16. doi: 10.1002/elps.201600197. Epub 2016 Jul 4. PMID: 27251892.

GenPlay 1.1.0 – Genome Analyzer and Browser

GenPlay 1.1.0

:: DESCRIPTION

GenPlay is an analyzer and browser for high-throughput data . GenPlay recognizes a wide variety of common genomic data formats from microarray- or sequencing-based platforms and offers a library of operations (normalization, binning, smoothing) to process raw data into visualizable tracks.

::DEVELOPER

Eric Bouhassira, Nicolas Fourel and Julien Lajugie

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • Java

:: DOWNLOAD

  GenPlay

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Aug 31. pii: btu588.
GenPlay Multi-Genome, a tool to compare and analyze multiple human genomes in a graphical interface.
Lajugie J, Fourel N, Bouhassira EE

Bioinformatics. 2011 Jul 15;27(14):1889-93.
GenPlay, a multipurpose genome analyzer and browser.
Lajugie J, Bouhassira EE.

GAAS 1.0.0.1 – Gene Array Analyzer Software

GAAS 1.0.0.1

:: DESCRIPTION

GAAS (Gene Array Analyzer Software) is an integrated software framework for efficient management, analysis and visualization of large amounts of gene expression data across replicated experiments. It is structured in management, analysis and visualization sections that allow dealing with several gene expression dataset formats, custom differential expression data analyses, suitable visualization, and storage of results.

The software performs pre-processing of gene expression data transforming any input data structure in MS-Excel format into a built-in database-based data structure in MS-Access format, perform fast differential gene expression analyses across multiple replica experiments.

GAAS is designed for a multi-user environment, enabling each user to store its own parameter values used to perform the analyses, and define data visualization schema and format of the output data.

::DEVELOPER

Pietro Cerveri, PhD  & Masseroli Marco, Ph.D

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

GAAS

:: MORE INFORMATION

Citation:

Masseroli M, Cerveri P, Pelicci PG, Alcalay M.
GAAS: Gene Array Analyzer Software for management, analysis and visualization of gene expression data.
Bioinformatics 2003 April 12; 19(6): 774-775.
[Abstract], [PDF], [PubMed].

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