What is inside
this site?
Go to THIS
PAGE to see statistics on the genome sequencing, assembly,
and gene modeling and download various analyses and datasets.
The genomes below,
including that of Danaus plexippus, have been analyzed by
the PHRINGE ("Phylogenetic Resources for the Interpretation
of Genomes") pipeline. Briefly described, PHRINGE creates a
graph with all inferred protein sequences as nodes, with edges formed
from distance scores calculated from their full length alignments,
then clusters these into gene families using a method that considers
the evolutionary relationships among the organisms, then performs
a phylogenetic analysis on each. This allows the most accurate possible
assignment of orthologous and paralogous relationships, inference
of retained gene function, and reconstruction of gene duplications
and losses. Users can see the multiple sequence alignments and phylogenetic
trees of all genes, compare intron-exon structures, and see the
relative arrangements of homologs across all genomes. See a summary
of the PHRINGE method, details
of the PHRINGE pipeline, or an explanation
of why it is important to use evolutionary analysis to find orthologs.
Every gene of each
animal has a "Detail Pages" with information such as its
position, length, and intron-exon structure, the most similar sequences,
with links, and the clusters (at various phylogenetic depths) to
which it has been assigned by PHRINGE. Find a Detail Page by gene
ID number, often obtained by searching
for a particular gene or by clicking on any particular gene
box on a Synteny Page. The cluster ID of each Detail Page is linked
to the corresponding "Cluster and Compare Page".
See an arbitrarily chosen example here.
Every cluster of
homologous genes has a "Cluster and Compare Page" with
information such as the multiple sequence alignment, comparison
of intron-exon structures, and the phylogeny of the member genes.
Find a Cluster and Compare Page from the cluster IDs on a Detail
Page of any member gene. See an arbitrarily chosen example here.
"Synteny Pages"
show an overview of the relative physical arrangements of homologous
genes for specified portions of specified genomes. Connecting lines
are red if there has been an inversion. Mouse over gene boxes for
more information. Click on any gene box to go to the corresponding
Detail Page. See an arbitrarily chosen example here.
Click on any numeral
in the "details" column of the table above to see which
cluster levels this taxon is found and a comparison of the numbers
of members of each gene family among all considered genomes. |
