Genomicus v30.01 - Gene Search

Here you can choose the oldest ancestor of your phylogenetic range of interest and the view you want to display by clicking on one of the following links.

PhyloView will show the conservation of the neighbourhood of the reference gene in the other species, according to the gene phylogenetic tree.
AlignView will align the gene order of the selected species, according to the species phylogenetic tree.

Root species for PMT2 (YAL023C) (Saccharomyces cerevisiae S288c)		AlignView depth	PhyloView depth
Fungi	~10 Mya	465 species	666 homologs (oldest homol.)
Dikarya	~10 Mya	420 species	629 homologs
Ascomycota	~10 Mya	307 species	490 homologs (dupl. node) 482 homologs (dupl. node) 176 homologs
saccharomyceta	~10 Mya	297 species	175 homologs
Saccharomycetales	~10 Mya	56 species	174 homologs (dupl. node) 172 homologs (dupl. node) 99 homologs (dupl. node) 67 homologs
Saccharomycetaceae	~10 Mya	29 species	66 homologs (dupl. node) 57 homologs (dupl. node) 52 homologs (dupl. node) 36 homologs (dupl. node) 20 homologs
Saccharomyces	~10 Mya	5 species	6 homologs (dupl. node) 3 homologs
Saccharomyces cerevisiae S288c	~0 Mya	1 species	1 homolog

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'

A more recent version of genomicus is available here