Genomicus v30.01 Title
Genomicus v30.01 Logo


DYOGEN group

web-code version: 2014-07-06
database version: 30.01


email logo Contact us.



IBENS Logo ENS Logo CNRS Logo ANCESTROME Logo

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: PMT2 , ANIA_00774, YGR134W.1

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. In contrast to Genomicus Vertebrates, Genomics Fungi does not yet display ancestral genome reconstructions.

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


Summary statistics of Genomicus version 30.01: (view species tree in pdf or newick)

Number of extant species313
Number of extant genes3153320
 
Number of ancestral species152
Number of ancestral genes2649825
Number of ancestral synteny blocks0

What's new in version 30.01 ?


Karyotype View and Matrix View

Karyotype View Matrix View


Other Genomicus Sites

Genomicus GenomicusPlants GenomicusMetazoa GenomicusProtists

Citing Genomicus:
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'