Tag: Gene Order

Syntenator 2 – Multiple Gene Order Alignments with a Gene-specific Scoring Function

Syntenator 2

:: DESCRIPTION

Syntenator represents genomes and alignments thereof as partial order graphs (POGs). These POGs are aligned by a dynamic programming approach employing a gene-specific scoring function. The scoring function reflects the level of protein sequence similarity for each possible gene pair. Our method consistently defines larger homologous regions in pairwise gene order alignments than nucleotide-level comparisons. Our method is superior to methods that work on predefined homology gene sets (as implemented in Blockfinder). Syntenator successfully reproduces 80% of the EnsEMBL man-mouse conserved syntenic blocks. The full potential of our method becomes visible by comparing remotely related genomes and multiple genomes. Gene order alignments potentially resolve up to 75% of the EnsEMBL 1:many orthology relations and 27% of the many:many orthology relations.

::DEVELOPER

BIMSB Bioinformatics Core.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / Mac OsX
  • Java 

:: DOWNLOAD

 Syntenator

:: MORE INFORMATION

Citation:

Algorithms Mol Biol. 2008 Nov 6;3:14.
Syntenator: multiple gene order alignments with a gene-specific scoring function.
Rödelsperger  C, Dieterich C.

YGOB v7 – Yeast Gene Order Browser

YGOB v7

:: DESCRIPTION

YGOB is an online tool for visualising the syntenic context of any gene from several yeast genomes.

::DEVELOPER

the Wolfe Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Genome Res. 2005 Oct;15(10):1456-61. Epub 2005 Sep 16.
The Yeast Gene Order Browser: combining curated homology and syntenic context reveals gene fate in polyploid species.
Byrne KP1, Wolfe KH.

MLGO – Maximum Likelihood for Gene Order Analysis

MLGO

:: DESCRIPTION

MLGO is a web server designed for genome rearrangement and gene order analysis. It can be used to infer a phylogeny from genome rearrangement and gene order data, and can also obtain an estimation of ancestral genomes, given an input tree. It can handle large scale data with the size ranges from mitochandrial to nuclear genomes. Besides rearrangements, it can also handle gene insertion, deletion and duplication.

::DEVELOPER

Jijun Tang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014 Nov 8;15(1):354. [Epub ahead of print]
MLGO: phylogeny reconstruction and ancestral inference from gene-order data.
Hu F, Lin Y, Tang J.

CYNTENATOR 20101005 – Progressive Gene Order Alignment of 17 Vertebrate Genomes

CYNTENATOR 20101005

:: DESCRIPTION

CYNTENATOR is a progressive gene order alignment software to identify genomic regions of conserved synteny over a large set of diverging species. CYNTENATOR does not depend on nucleotide-level alignments and a priori homology assignment.

::DEVELOPER

Dieterich lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 CYNTENATOR

:: MORE INFORMATION

Citation:

PLoS One. 2010 Jan 28;5(1):e8861.
CYNTENATOR: progressive gene order alignment of 17 vertebrate genomes.
Rödelsperger  C, Dieterich C.

ProCARs 2016 – Progressive Reconstruction of Ancestral Gene Orders

ProCARs 2016

:: DESCRIPTION

ProCARs is a program used to reconstruct Ancestral gene orders as CARs (Contiguous Ancestral Regions) with a progressive homology-based method. The method runs from a phylogeny tree (without branch lengths needed) with a marked ancestor and a block file.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • Python

:: DOWNLOAD

ProCARs

:: MORE INFORMATION

Citation:

Perrin A, Varré JS, Blanquart S, Ouangraoua A.
ProCARs: Progressive Reconstruction of Ancestral Gene Orders.
BMC Genomics. 2015;16 Suppl 5(Suppl 5):S6. doi: 10.1186/1471-2164-16-S5-S6. Epub 2015 May 26. PMID: 26040958; PMCID: PMC4460626.

SHOT 2.0 – Shared Ortholog and Gene Order Tree Reconstruction Tool

SHOT 2.0

:: DESCRIPTION

SHOT is a web server for the classification of genomes on the basis of shared gene content or the conservation of gene order that reflects the dominant, phylogenetic signal in these genomic properties. In general, the genome trees are consistent with classical gene-based phylogenies, although some interesting exceptions indicate massive horizontal gene transfer. SHOT is a useful tool for analysing the tree of life from a genomic point of view

::DEVELOPER

Bork Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

SHOT: a web server for the construction of genome phylogenies.
Korbel JO, Snel B, Huynen MA, Bork P
Trends Genet. 2002 Mar; 18(3): 158-62. PubMed: 11858840.

DILTAG – Inferring the Evolutionary History of Gene Clusters from Phylogenetic and Gene Order Data

DILTAG

:: DESCRIPTION

DILTAG is an algorithm allowing to infer a set of optimal evolutionary histories for a gene cluster in a single species, according to a general cost model involving variable length duplications (in tandem or inverted), deletions, and inversions.

::DEVELOPER

NADIA EL-MABROUK

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

M. Lajoie, D. Bertrand and N. El-Mabrouk.
Inferring the Evolutionary History of Gene Clusters from Phylogenetic and Gene Order Data.
Mol Biol Evol. 2010 Apr;27(4):761-72. doi: 10.1093/molbev/msp271