Genomicus v90.01 Title
Genomicus v90.01 Logo


DYOGEN group

web-code version: 2017-06-13
database version: 90.01
Tweets by GenomicusDB

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Enter a gene name or a CNE name (Ensembl nomenclature or approved gene symbol)
You can restrict the search to one species (ancestral or modern).

Search by gene name
Search by CNE name
BLAST Search
Default view
Custom view
 

Selected examples: fgf1a, Phox2B, egr2, AMHR2, RegHsa4027615 . More details on examples can be found here

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.

All the data on extant species displayed in this browser are from Ensembl.


Summary statistics of Genomicus version 90.01: (view species tree in pdf or newick)

Number of extant species87
Number of extant genes1613382
 
Number of ancestral species72
Number of ancestral genes1399291
Number of ancestral synteny blocks35888

What's new in version 90.01 ?


Multi-genomes comparison
Karyotype ViewPhyloview
Multi Karyotype View Phyloview

Pairwise genomes comparaison
Phyldiag ViewMatrix ViewKaryotype View
Phyldiag View Matrix View Karyotype View


All Genomicus Sites

GenomicusVertebrates 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'