Geptop 2.0 – Gene Essentiality Prediction tool for COMPLETE-GENOME based on Orthology and Phylogeny

Geptop 2.0

:: 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

Microbe and Drug Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • Python
  • BioPython

:: DOWNLOAD

 Geptop

:: MORE INFORMATION

Citation

Wen QF, Wei W, Guo FB.
Geptop 2.0: Accurately Select Essential Genes from the List of Protein-Coding Genes in Prokaryotic Genomes.
Methods Mol Biol. 2022;2377:423-430. doi: 10.1007/978-1-0716-1720-5_23. PMID: 34709630.

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.

OrthoInspector 3.0 – Rapid Detection of Orthology and Inparalogy Relations between Different Species

OrthoInspector 3.0

:: 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

Complex Systems and Translational Bioinformatics team – ICube laboratory

:: SCREENSHOTS

OrthoInspector

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java
  • MySQL

:: DOWNLOAD

 OrthoInspector

:: MORE INFORMATION

Citation:

Nevers Y, Kress A, Defosset A, Ripp R, Linard B, Thompson JD, Poch O, Lecompte O.
OrthoInspector 3.0: open portal for comparative genomics.
Nucleic Acids Res. 2019 Jan 8;47(D1):D411-D418. doi: 10.1093/nar/gky1068. PMID: 30380106; PMCID: PMC6323921.

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.

Proteinortho 6.30 – Orthology Detection Tool

Proteinortho 6.30

:: 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.

NCG 6.0 – Web Resource to Analyze Duplicability, Orthology and Network Properties of Cancer Genes

NCG 6.0

:: 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.

OrthoClust – Orthology-based Network Framework for Clustering data across multiple Species

OrthoClust

:: DESCRIPTION

OrthoClust is a clustering algorithm built on a multilayer network framework. It concatenates networks from individual species by their orthology relationships, arriving at a multiplex network. By optimizing the a generalized modularity function, OrthoClust returns a set of modules that could be either conserved or species-specific.

::DEVELOPER

Gerstein Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

OrthoClust

:: MORE INFORMATION

Citation:

Genome Biol. 2014 Aug 28;15(8):R100. doi: 10.1186/gb-2014-15-8-r100.
OrthoClust: an orthology-based network framework for clustering data across multiple species.
Yan KK, Wang D, Rozowsky J, Zheng H, Cheng C, Gerstein M.

OrthoXML 0.3 / SeqXML 0.4 – XML standards for Orthology and Sequence Information

OrthoXML 0.3 / SeqXML 0.4

:: DESCRIPTION

OrthoXML is designed broadly to allow the storage and comparison of orthology data from any ortholog database. It establishes a structure for describing orthology relationships while still allowing flexibility for database-specific information to be encapsulated in the same format.

The SeqXML schema (XSD) defines the skeletal structure of the sequence files and allows one to set constraints for each type of data it contains: for example, one can limit a DNA sequence to consist only of {A,G,C,T,N}. If one then tries to import a DNA sequence containing a ‘Z’, this error will be detected automatically by any XML validator.

:: DEVELOPER

Sonnhammer Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

OrthoXML  / SeqXML

:: MORE INFORMATION

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