Biology Reference
In-Depth Information
Table 2.
The resources, features, and links to a selection of public databases,
reflecting the principal approaches to the delineation of orthologous and paralogous
relationships from large-scale genomic data.
Resource
Features
Website
InParanoid and
BLAST, RBH, eukaryotes,
http://inparanoid.cgb.ki.se
MultiParanoid
automatic
COG/KOG/
BLAST, RBH,
http://www.ncbi.nlm.
arCOG
semi-curated
nih.gov/COG
OrthoDB
Smith-Waterman, RBH,
http://cegg.unige.ch/
hierarchical, eukaryotes,
orthodb
automatic
Ensembl Compara
Smith-Waterman, ML
http://www.ensembl.org
tree reconciliation,
vertebrates, automatic
eggNOG
Smith-Waterman, RBH
http://eggnog.embl.de
triangles, Semi-
hierarchical,
automatic
OrthoMCL
BLAST, Markov cluster
http://www.cbil.upenn.
algorithm, automatic
edu/gene-family
OPTIC
BLAST, Dn/Ds distance,
http://genserv.anat.ox.
automatic
ac.uk/clades
SYNERGY
FASTA, synteny-guided
http://www.broad.mit.
RBH, tree
edu/regev/orthogroups
reconstruction, fungi
orthologs enables investigations into the evolution of gene structure in
terms of the properties of their constituent exons and introns.
Probabilistic modeling of intron evolution using orthologs suggests a
balance of intron gain and loss across all lineages, with elevated intron
gain occurring very early in the eukaryotic phylogeny and several lineages
such as fungi and insects later experiencing elevated intron losses.
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Gene structure comparisons have also revealed the importance of
alternative splicing as a major transcript diversification mechanism in ani-
mals to produce different protein isoforms from a single gene. Estimates
