A more recent version of genomicus is available here

 
Genomicus v105.01 Title
Genomicus v105.01 Logo


DYOGEN group

web-code version: 2021-08-15
database version: 105.01
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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
Search by CNE name
BLAST Search
TreePattern Search
Default view
Custom view
 

Selected examples: fgf1a, Phox2B, egr2, 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 105.01: (view species tree in pdf or newick)

Number of extant species200
Number of extant genes4303993
 
Number of ancestral species196
Number of ancestral genes4624213
Number of ancestral synteny blocks83342

WARNING: Genomicus is based on data from Ensembl, and since the release of version 94, Ensembl has changed its phylogenetic trees reconstruction approach, causing large gene families (> ~400 homologs) to be split in several smaller families. Some paralogy relationships may therefore be lost.

To acces the most recent version of Genomicus without these paralogy issues, please use release Genomicus93.

 
What's new in version 105.01 ?




Other Genomicus Sites

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

Citing Genomicus:
Genomicus in 2022: comparative tools for thousands of genomes and reconstructed ancestors .
Nga Thi Thuy Nguyen, Pierre Vincens, Jean-Francois Dufayard, Hugues Roest Crollius, Alexandra Louis. Nucleic Acids Research 2021;doi: 10.1093/nar/gkab1091

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'