Genomicus v01.01 Title
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DYOGEN group

web-code version: 2017-06-13
database version: 01.01


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

Search by gene name
 Default view
Custom view		  

Selected example: BL22073

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 and from the European Branchiostoma lanceolatum consortium .


Summary statistics of Genomicus version 01.01: (view species tree in pdf or newick)

Number of extant species12
Number of extant genes281605
 
Number of ancestral species11
Number of ancestral genes219021
Number of ancestral synteny blocks9610

What's new in version 01.01 ?
European amphioxus Welcome to the European Amphioxus Genomicus Server.


Multi-genomes comparison
PhyloViewAlignView
Phyloview AlignView
Pairwise genomes comparaison
Phyldiag ViewMatrix ViewKaryotype View
Phyldiag View Matrix View Karyotype View


Other Genomicus Sites

GenomicusVertebrates GenomicusProtists GenomicusPlants GenomicusMetazoa GenomicusFungi

Citing Genomicus:
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'