Genomicus v27.01 Logo

Genomicus v27.01 Title

web-code version: 2019-11-04
database version: 27.01
Tweets by South Green

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Powered by Genomicus (IBENS)

Enter a gene name
You can restrict the search to one species (ancestral or modern).

Search by gene name
Default view
Custom view
 

Selected examples: Seita.3G233000.1, Sobic.009G148000.1, WRKY

Genomicus is a genome browser that enables users to navigate in genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Once a query gene has been entered, it is displayed in its genomic context in parallel to the genomic context of all its orthologous and paralogous copies in all the other sequenced metazoan genomes. Moreover, Genomicus stores and displays the predicted ancestral genome structure in all the ancestral species within the phylogenetic range of interest.


Summary statistics of Genomicus version 27.01: (view species tree in pdf or newick)

Number of extant species27
Number of extant genes1040086
 
Number of ancestral species17
Number of ancestral genes810245
Number of ancestral synteny blocks0

Website Data Usage Policy in version 27.01 ?
Version 27.01 of Genomicus (made by South Green on 27 plant species) adheres to the Toronto Agreement on prepublication data release for all data deposited.
We (the coconut data producers) encourage the pre-publication use of these data in accordance with the Toronto data sharing principles described at https://www.nature.com/articles/461168a.
Questions about data use should be directed to Dr. St├ęphanie Bocs (stephanie.sidibe-bocs[AT]cirad.fr).
By accessing these resources, data users agree that the following analyses are reserved for first description by the data producers.




Other Genomicus Sites

GenomicusVertebrates Genomicus-Pre-2R GenomicusPlants
GenomicusMetazoa GenomicusFungi GenomicusProtists
GenomicusTrout GenomicusTunicates GenomicusAmphioxus

Citing Genomicus:
Genomicus 2018: karyotype evolutionary trees and on-the-fly synteny computing.
Nga Thi Thuy Nguyen, Pierre Vincens, Hugues Roest Crollius, Alexandra Louis. Nucleic Acids Research 2017;doi: 10.1093/nar/gkx1003
Genomicus update 2015: KaryoView and MatrixView provide a genome-wide perspective to multispecies comparative genomics .
Alexandra Louis; Nga Thi Thuy Nguyen; Matthieu Muffato; Hugues Roest Crollius Nucleic Acids Research 2014;doi: 10.1093/nar/gku1112
Genomicus: five genome browsers for comparative genomics in eukaryota.
Alexandra Louis; Matthieu Muffato; Hugues Roest Crollius. Nucleic Acids Research 2012; doi: 10.1093/nar/gks1156

Advanced Options
-evalue <Real>
Expectation value (E) threshold for saving hits
Default = '10'
-word_size <Integer, >=2>
Word size for wordfinder algorithm
Default = '3'
-gapopen <Integer>
Cost to open a gap
Default = '11'
-gapextend <Integer>
Cost to extend a gap
Default = '1'
-matrix <String>
Scoring matrix name (normally BLOSUM62)
-threshold <Real, >=0>
Minimum word score such that the word is added to the BLAST lookup table
Default = '11'
-window_size <Integer, >=0>
Multiple hits window size, use 0 to specify 1-hit algorithm
Default = '40'