Tag: Organism

gNOMO – Host and Microbiome analysis of non-model Organisms

gNOMO

:: DESCRIPTION

gNOMO is a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms.

::DEVELOPER

gNOMO team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

gNOMO

:: MORE INFORMATION

Citation

Muñoz-Benavent M, Hartkopf F, Van Den Bossche T, Piro VC, García-Ferris C, Latorre A, Renard BY, Muth T.
gNOMO: a multi-omics pipeline for integrated host and microbiome analysis of non-model organisms.
NAR Genom Bioinform. 2020 Aug 5;2(3):lqaa058. doi: 10.1093/nargab/lqaa058. Erratum in: NAR Genom Bioinform. 2020 Oct 09;2(4):lqaa083. PMID: 33575609; PMCID: PMC7671378.

COMODO 2.0 – Identify Conserved Coexpression Modules between Organisms

COMODO 2.0

:: DESCRIPTION

COMODO (COnserved MODules across Organisms) is a coclustering procedure to identify conserved expression modules between two species. The method uses as input microarray data and a gene homology map and provides as output pairs of conserved modules and searches for the pair of modules for which the number of sharing homologs is statistically most significant relative to the size of the linked modules.

::DEVELOPER

Kathleen Marchal

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 COMODO

:: MORE INFORMATION

Citation

COMODO: an adaptive coclustering strategy to identify conserved coexpression modules between organisms.
Zarrineh P, Fierro AC, Sánchez-Rodríguez A, De Moor B, Engelen K, Marchal K.
Nucleic Acids Res. 2011 Apr;39(7):e41. Epub 2010 Dec 10.

OrthoNets 1.0 – Simultaneous Visual Analysis of Orthologs and their Interaction Neighborhoods across different organisms

OrthoNets 1.0

:: DESCRIPTION

OrthoNets provides various information about the proteins and interactions – including domain architectures (bottom of figure 1), protein and gene aliases, pubmed identifiers of the publications supporting the interactions, and the experiment type used to detect the interaction. Here the view is focused on the RNA polymerase enzyme LEO1 – so that only the LEO1 node and its recorded interaction partners are displayed.

::DEVELOPER

The Wodak Lab

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 OrthoNets

:: MORE INFORMATION

Citation

Yanqi Hao, Anna Merkovitch, James Vlasblom, Shuye Pu, Andrei L. Turinsky, Denitza Roudeva, Brian Turner, Jack Greenblatt, Shoshana J. Wodak.
OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms.
Bioinformatics. 2011 Mar 15;27(6):883-4. Epub 2011 Jan 20.

MARRVEL v2 – Model organism Aggregated Resources for Rare Variant ExpLoration

MARRVEL v2

:: DESCRIPTION

MARRVEL aims to facilitate the use of public genetic resources to prioritize rare human gene variants for study in model organisms. To automate the search process and gather all the data in a simple display we extract data from human data bases (OMIM, ExAC, Geno2MP, DGV, and DECIPHER) for efficient variant prioritization. The protein sequences for six organisms (S. cerevisiae, C. elegans, D. melanogaster, D. rerio, M. musculus, and H. sapiens) are aligned with highlighted protein domain information via collaboration with DIOPT.

:: DEVELOPER

Liu Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Wang J, Al-Ouran R, Hu Y, Kim SY, Wan YW, Wangler MF, Yamamoto S, Chao HT, Comjean A, Mohr SE; UDN, Perrimon N, Liu Z, Bellen HJ.
MARRVEL: Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome.
Am J Hum Genet. 2017 Jun 1;100(6):843-853. doi: 10.1016/j.ajhg.2017.04.010. Epub 2017 May 11. PMID: 28502612; PMCID: PMC5670038.

Semantic Body Browser 1.6.2 – Graphically Exploring an Organism’s Body

Semantic Body Browser 1.6.2

:: DESCRIPTION

The Semantic Body Browser (SBB) is a web application for intuitively exploring the body of an organism from the organ to the sub-cellular level and visualising expression profiles by means of semantically annotated illustrations. It is used to comprehend biological and medical data related to the different body structures while relying on the strong pattern recognition capabilities of human users.

::DEVELOPER

SBB team

:: SCREENSHOTS

N/A

::REQUIREMENTS

:: DOWNLOAD

 Semantic Body Browser

:: MORE INFORMATION

Citation

Semantic Body Browser: Graphical exploration of an organism and spatially resolved expression data visualisation.
Lekschas F, Stachelscheid H, Seltmann S, Kurtz A.
Bioinformatics. 2014 Oct 24. pii: btu707.

ChimeraUGEM 1.01 – Unsupervised Gene Expression Modeling in any given Organism

ChimeraUGEM 1.01

:: DESCRIPTION

ChimeraUGEM provides tools for the analysis of gene sequences (coding and non-coding), as well as the design of protein coding sequences for optimized expression, based on the Chimera algorithms and codon usage optimization.

::DEVELOPER

Tamir Tuller’s Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • MatLab

:: DOWNLOAD

ChimeraUGEM

:: MORE INFORMATION

Citation

Diament et al.
ChimeraUGEM: unsupervised gene expression modeling in any given organism.
Bioinformatics, 35 (18), 3365-3371 2019 Sep 15

FOCUS 1.4 – A model to Identify Organisms present in Metagenomes

FOCUS 1.4

:: DESCRIPTION

FOCUS, an innovative and agile composition based using non-negative least squares to profile and report abundant organisms present in me-tagenomic samples and their relative abundance without sequence length dependencies.

::DEVELOPER

the Edwards Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac OsX / Linux
  • Python

:: DOWNLOAD

 FOCUS

:: MORE INFORMATION

Citation:

Silva, G. G. Z., D. A. Cuevas, B. E. Dutilh, and R. A. Edwards, 2014
FOCUS: an alignment-free model to identify organisms in metagenomes using non-negative least squares.
PeerJ, 2, e425, doi:10.7717/peerj.425.

PHYLDOG 2.0beta – Organism and Gene PHYlogenies Modeling Gene Duplications and Losses

PHYLDOG 2.0beta

:: DESCRIPTION

Phyldog is a program made to simultaneously build gene and species trees when gene families have undergone duplications and losses.

::DEVELOPER

Bastien Boussau

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Boost libraries
  • Bio++

:: DOWNLOAD

 PHYLDOG

:: MORE INFORMATION

Citation:

Genome Res. 2013 Feb;23(2):323-30. doi: 10.1101/gr.141978.112.
Genome-scale coestimation of species and gene trees.
Boussau B, Szöllosi GJ, Duret L, Gouy M, Tannier E, Daubin V.

MORPHIN – Model Organisms Projected on a Human Integrated Gene Network

MORPHIN

:: DESCRIPTION

MORPHIN is a web-based bioinformatics tool to study human diseases using model organism genes.

::DEVELOPER

Network Biomedicine Laboratory  at Yonsei University, Korea and the Marcotte Lab at University of Texas at Austin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

MORPHIN: a web tool for human disease research by projecting model organism biology onto a human integrated gene network.
Hwang S, Kim E, Yang S, Marcotte EM, Lee I.
Nucleic Acids Res. 2014 Jul;42(Web Server issue):W147-53. doi: 10.1093/nar/gku434.

Bugs 2.0 – Simulate Bacteria-like Organism Growth

Bugs 2.0

:: DESCRIPTION

Bugs is a simple genetic algorithm program that simulates bacteria-like organisms which move about in a field of “algae” that they eat by moving over them. When they eat enough of the algae, they reproduce by division; if they don’t eat enough, they die. Over time, the initial aimless bugs will evolve into efficient foragers scouring their world for fresh algae.

::DEVELOPER

The Queller/Strassmann Research Group at Washington University in St. Louis

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac

:: DOWNLOAD

 Bugs

:: MORE INFORMATION