Tag: Synteny

Cinteny – Server for Synteny Identification and Analysis of Genome Rearrangement

Cinteny

:: DESCRIPTION

Cinteny is a flexible and efficient tool for analysis of synteny and evolutionary distances in terms of genome rearrangements (the reversal distance) for multiple genomes. In addition to annotated genomes, which are available for interactive browsing and assessment of synteny and evolutionary distances in terms of orthologous genes, Cinteny can be used with user provided discrete objects, such as sequence tags or other evolutionarily conserved markers.

:: SCREENSHOTS

N/A

::DEVELOPER

Meller Lab

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2007 Mar 8;8:82.
Cinteny: flexible analysis and visualization of synteny and genome rearrangements in multiple organisms.
Sinha AU1, Meller J.

Satsuma2 – Whole-genome Synteny Aligner

Satsuma2

:: DESCRIPTION

Satsuma is a whole-genome synteny alignment program. It takes two genomes, computes alignments, and then keeps only the parts that are orthologous, i.e. following the conserved order and orientation of features, such as protein coding genes, non-coding genes, or neutral sequences.

Satsuma2 is an optimised version of Satsuma, a tool to reliably align large and complex DNA sequences providing maximum sensitivity (to find all there is to find), specificity (to only find real homology) and speed (to accomodate the billions of base pairs in vertebrate genomes).

::DEVELOPER

Grabherr Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX
  • C++ Compiler

:: DOWNLOAD

Satsuma2

:: MORE INFORMATION

Citation

Grabherr MG, Russell P, Meyer M, Mauceli E, Alfoldi J, Di Palma F, Lindblad-Toh K.
Genome-wide synteny through highly sensitive sequence alignment: Satsuma.
Bioinformatics. 2010 May 1;26(9):1145-51. Epub 2010 Mar 5

Insyght – Conserved Synteny Homolog Browser

Insyght

:: DESCRIPTION

Insyght is a browser that helps navigate among abundant homologies, syntenies and genes annotations.

::DEVELOPER

Insyght team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Synchronized navigation and comparative analyses across Ensembl complete bacterial genomes with INSYGHT.
Lacroix T, Thérond S, Rugeri M, Nicolas P, Gendrault A, Loux V, Gibrat JF.
Bioinformatics. 2015 Nov 24. pii: btv689.

Proteny 0.1 – Analyze Synteny at the Protein Level

Proteny 0.1

:: DESCRIPTION

Proteny is a tool to analyze and visualize synteny at the protein level between two organisms

::DEVELOPER

The Delft Bioinformatics Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

 Proteny

:: MORE INFORMATION

Citation

Proteny: Discovering and visualizing statistically significant syntenic clusters at the proteome level.
Gehrmann T, Reinders MJ.
Bioinformatics. 2015 Jun 27. pii: btv389.

Synteny – Investigate Sequence Conservation between Species

Synteny

:: DESCRIPTION

Synteny is a tool to investigate sequence conservation between species.

::DEVELOPER

Krawetz Lab

:: SCREENSHOTS

Synteny

:: REQUIREMENTS

  • Windows 

:: DOWNLOAD

 Synteny

:: MORE INFORMATION

Citation

Martins R. P., Krawetz S. A.
Nuclear organization of the protamine locus. Reproduction in Domestic Ruminants,
VI, J. L. Juengel, J. F. Murray, M. F. Smith. Nottingham University Press, NottinghamUK 2007b; 1-12.