Proteinortho 5.13 – Orthology Detection Tool

Proteinortho 5.13

:: DESCRIPTION

Proteinortho predicts (co-)orthologous proteins within different species.

::DEVELOPER

Bioinformatics Leipzig

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Proteinortho

:: MORE INFORMATION

Citation

Lechner et al (2011).
Proteinortho: Detection of (Co-)Orthologs in Large-Scale Analysis.
BMC Bioinformatics 2011 Apr 28;12(1):124.

OrthoInspector 2.14 – Rapid Detection of Orthology and Inparalogy Relations between Different Species

OrthoInspector 2.14

:: DESCRIPTION

OrthoInspector is a software system incorporating an original algorithm for the rapid detection of orthology and inparalogy relations between different species. IIn addition, several visualization tools have been developed to facilitate in-depth studies based on these predictions. It is made available as an independent software suite that can be downloaded and installed for local use. Command line querying facilitates the integration of the software in high throughput processing pipelines and a graphical interface provides easy, intuitive access to results for the non-expert.

::DEVELOPER

LBGI : Laboratoire de bioinformatique et de génomique intégratives

:: SCREENSHOTS

OrthoInspector

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java
  • MySQL

:: DOWNLOAD

 OrthoInspector

:: MORE INFORMATION

Citation:

OrthoInspector 2.0: software and database updates.
Linard B, Allot A, Schneider R, Morel C, Ripp R, Bigler M, Thompson JD, Poch O, Lecompte O.
Bioinformatics. 2014 Oct 1. pii: btu642.

BMC Bioinformatics. 2011 Jan 10;12:11. doi: 10.1186/1471-2105-12-11.
OrthoInspector: comprehensive orthology analysis and visual exploration.
Linard B, Thompson JD, Poch O, Lecompte O.

Geptop – Gene Essentiality Prediction tool for COMPLETE-GENOME based on Orthology and Phylogeny

Geptop

:: DESCRIPTION

Geptop is a webserver, which first provides a platform to detect essential gene sets over bacterial species, by comparing orthology and phylogeny of query protein sets with essential gene datasets determined experimentally (from DEG database).

::DEVELOPER

Group of Computational,Comparative Evolutionary and Functional Genomics (CEFG)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • Python
  • BioPython

:: DOWNLOAD

 Geptop

:: MORE INFORMATION

Citation

PLoS One. 2013 Aug 15;8(8):e72343. doi: 10.1371/journal.pone.0072343. eCollection 2013.
Geptop: a gene essentiality prediction tool for sequenced bacterial genomes based on orthology and phylogeny.
Wei W1, Ning LW, Ye YN, Guo FB.

NCG 4.0 – Web Resource to Analyze Duplicability, Orthology and Network Properties of Cancer Genes

NCG 4.0

:: DESCRIPTION

NCG (Network of Cancer Genes) is a web resource of the network of cancer genes in the era of massive mutational screenings of cancer genomes

::DEVELOPER

the Ciccarelli Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

Nucleic Acids Res. 2012 Jan;40(Database issue):D978-83. doi: 10.1093/nar/gkr952.
Network of Cancer Genes (NCG 3.0): integration and analysis of genetic and network properties of cancer genes.
D’Antonio M, Pendino V, Sinha S, Ciccarelli FD.