Genomicus v24.01 Title
Genomicus v24.01 Logo


DYOGEN group

web-code version: 2014-09-19
database version: 24.01


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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
BLAST Search
Default view
Custom view
 

Selected examples: BRADI2G34810, PHYA, TUBB1, GRMZM2G028033.

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 EnsemblGenome Plant, Phytozome, and specific servers. and .


Summary statistics of Genomicus version 24.01: (view species tree in pdf or newick)

Number of extant species48
Number of extant genes1645025
 
Number of ancestral species36
Number of ancestral genes1541702
Number of ancestral synteny blocks50671

What's new in version 24.01 ?
Warning: Arabidopsis thaliana genes often possess many alternative names in addition to the TAIR locus name. Currently such genes may only be queried using the TAIR locus name or a single alternative name, identical to the main name used in EnsemblGenome.
We apologise for the inconvenience.


Karyotype View and Matrix View

Karyotype View Matrix View


Other Genomicus Sites

Genomicus GenomicusProtists 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'