GenomicusPlants v49.01

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
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Selected examples: PHYA, PGSC0003DMG400006482, LIR1.

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 plants 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 EnsemblPlants.

Summary statistics of Genomicus version 49.01: (view species tree in pdf or newick)


Number of extant species	99
Number of extant genes	3262124
Number of ancestral species	59
Number of ancestral genes	2277838
Number of ancestral synteny blocks	96373

What's new in version 49.01 ?

Version 49.01 of Genomicus stores data from EnsemblGenomes Plants release 49

Other Genomicus Sites

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

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'