OrthoGNC 3.0 – Accurate Identification of Orthologs based on Gene Neighborhood Conservation

OrthoGNC 3.0

:: DESCRIPTION

OrthoGNC is a software for predicting accurate pairwise orthology relations based on gene neighborhood conservation.

::DEVELOPER

School of Biological Sciences, Iran

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • Java

:: DOWNLOAD

OrthoGNC

:: MORE INFORMATION

Citation

Genomics Proteomics Bioinformatics. 2017 Dec;15(6):361-370. doi: 10.1016/j.gpb.2017.07.002.
OrthoGNC: A Software for Accurate Identification of Orthologs Based on Gene Neighborhood Conservation.
Jahangiri-Tazehkand S, Wong L, Eslahchi C.

ProteinPathTracker – Find Orthologs Selected to study the Evolutionary Path of Protein

ProteinPathTracker

:: DESCRIPTION

ProteinPathTracker is an easy-to-use web tool that allows to track the evolutionary history of a query protein. The tracking strategy is performed on different proteomes located in a taxa path of your choice. For each of the intermediate taxa in the selected path, you can select the proteome in which we will look for homologs.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2018 Nov 19;19(1):431. doi: 10.1186/s12859-018-2457-y.
Automated selection of homologs to track the evolutionary history of proteins.
Mier P, Pérez-Pulido AJ, Andrade-Navarro MA.

orthoFind – Obtain Orthologs and Paralogs of Protein Sequence

orthoFind

:: DESCRIPTION

orthoFind searchs for homologous and orthologous proteins at a genomics level. It allows a quick search given one or more query sequences, and it can search either Swiss-Prot, a collection of reference proteomes, or user datasets. These results are accompanied with a simple functional annotation, including a study of their domain architecture.

::DEVELOPER

Computational Biology and Data Mining (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2015 Dec 1;10(12):e0143906. doi: 10.1371/journal.pone.0143906.
orthoFind Facilitates the Discovery of Homologous and Orthologous Proteins.
Mier P, Andrade-Navarro MA, Pérez-Pulido AJ.

HaMStR 13.2.6 – Hidden Markov Model based Search for Orthologs using Reciprocit

HaMStR 13.2.6

:: DESCRIPTION

HaMStR (Hidden Markov Model based Search for Orthologs using Reciprocity)is a Hidden Markov Model based search tool to screen EST sequence data for the presence of putative orthologs to a pre-defined set of genes.

::DEVELOPER

 the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 HaMStR

:: MORE INFORMATION

Citation:

BMC Evol Biol. 2009 Jul 8;9:157.
HaMStR: profile hidden markov model based search for orthologs in ESTs.
Ebersberger I, Strauss S, von Haeseler A.

inGeno 0.6 – Integrated Genome and Ortholog Viewer

inGeno 0.6

:: DESCRIPTION

inGeno is designed for genome sequence comparisons, which has been proven to be powerful, in particular to prokaryotic genomes of close phylogenetic distances. The original purpose of this software is to user-friendly visualize the corresponding relationships between orthologous genes. Step by step, a series of algorithms are implemented and integrated together, thus enable a noise-reducing process, a locus collinear block recognition and a text-mining step, which are helpful for users to extract biological information precisely.

::DEVELOPER

Department of BioinformaticsBiocenterUniversity of Würzburg, Germany

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • Java

:: DOWNLOAD

 inGeno

:: MORE INFORMATION

Citation

inGeno–an integrated genome and ortholog viewer for improved genome to genome comparisons.
Liang C, Dandekar T.
BMC Bioinformatics. 2006 Oct 20;7:461.

LOFT 1.0.5 – Orthology Prediction at Scalable Resolution by Phylogenetic Tree analysis

LOFT 1.0.5

:: DESCRIPTION

LOFT (Levels of Orthology From Trees) assigns hierarchical orthology numbers to genes based on a phylogenetic tree. To decide upon speciation and gene duplication events in a tree LOFT can be instructed either to perform classical species-tree reconciliation or to use the species overlap between partitions in the tree. The hierarchical orthology numbers assigned by LOFT effectively summarize the phylogenetic relations between genes. The resulting high-resolution orthologous groups are depicted in colour, facilitating visual inspection of (large) trees. A benchmark for orthology prediction, that takes into account the varying levels of orthology between genes, shows that the phylogeny-based high-resolution orthology assignments made by LOFT are reliable.

::DEVELOPER

the Centre for Molecular and Biomolecular Informatics,the CMBI.

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

  LOFT

:: MORE INFORMATION

Citation

René TJM van der Heijden,
Orthology prediction at scalable resolution by phylogenetic tree analysis,
BMC Bioinformatics 2007, 8:83

BUSCO v1.1b1 – Assessing Genome Assembly and Annotation Completeness with Single-copy Orthologs

BUSCO v1.1b1

:: DESCRIPTION

BUSCO completeness assessment employs sets of Benchmarking Universal Single-Copy Orthologs from OrthoDB to provide quantitative measures of the completeness of genome assemblies, annotated gene sets, and transcriptomes in terms of expected gene content.

::DEVELOPER

Zdobnov’s Computational Evolutionary Genomics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python
  • NCBI BLAST+
  • HMMER (HMMER 3.1b2)
  • Augustus 3.0.x

:: DOWNLOAD

 BUSCO

:: MORE INFORMATION

Citation

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs.
Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM.
Bioinformatics. 2015 Jun 9. pii: btv351.

DODO – DOmain based Detection of Orthologs

DODO

:: DESCRIPTION

DODO is an efficient method to detect orthologs in genomes. Given protein sequences of interested genomes, DODO can identify orthologous relationship based on protein domain information.

::DEVELOPER

Transcriptome Discovery Laboratory

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 DODO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Oct 15;11 Suppl 7:S6. doi: 10.1186/1471-2105-11-S7-S6.
DODO: an efficient orthologous genes assignment tool based on domain architectures. Domain based ortholog detection.
Chen TW1, Wu TH, Ng WV, Lin WC.

SPOCS 1.0.10 – Graph-based Ortholog/Paralog Prediction tool

SPOCS 1.0.10

:: DESCRIPTION

SPOCS (Species Paralogy and Orthology Clique Solver) is a graph-based ortholog/paralog prediction tool that will predict orthologs and paralogs given a set of prokaryotic proteomes (the set of proteins encoded by a genome). The software will take a set of protein fasta files (one per species genome), and an optional additional fasta to serve as an outgroup (a species that should be more distantly related to the species of interest than any of the species of interest are to each other).

::DEVELOPER

Computational Biology & Bioinformatics ,Pacific Northwest National Laboratory

:: SCREENSHOTS

SPOCS

:: REQUIREMENTS

  • Linux/ MacOsX
  • C++ Compiler
  • NCBI BLAST

:: DOWNLOAD

 SPOCS

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Oct 15;29(20):2641-2. doi: 10.1093/bioinformatics/btt454.
SPOCS: software for predicting and visualizing orthology/paralogy relationships among genomes.
Curtis DS, Phillips AR, Callister SJ, Conlan S, McCue LA.

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.