Comparative Genomics

Information Data Comparative Genomics

BlastZ-net Analysis

BlastZ-net (Schwartz S et al., Genome Res.;13(1):103-7, Kent WJ et al., Proc Natl Acad Sci U S A., 2003;100(20):11484-9) alignments are provided for closely related pairs of species. The alignments are the results of post-processing the raw BlastZ results. In the first step, original blocks are chained according to their location in both genomes. The netting process chooses for the reference species the best sub-chain in each region. The reference species in the BlastZ-net alignments is defined in this table:

	H.sap	P.tro	M.mul	M.mus	R.nor	C.fam	B.tau	M.dom	G.gal	T.rub	T.nig	C.int	C.sav	D.nov	E.tel	L.afr	O.cun
*Homo sapiens*	H.sap
*Pan troglodytes*	YES (on H.sap)	P.tro
*Macaca mulatta*	YES (on H.sap)	-	M.mul
*Mus musculus*	YES (on H.sap)	-	-	M.mus
*Rattus norvegicus*	YES (on R.nor)	-	-	YES (on R.nor)	R.nor
*Canis familiaris*	YES (on C.fam)	-	-	YES (on C.fam)	-	C.fam
*Bos taurus*	YES (on H.sap)	-	-	-	-	-	B.tau
*Monodelphis domestica*	YES (on H.sap)	-	-	-	-	-	-	M.dom
*Gallus gallus*	YES (on H.sap)	-	-	-	-	-	-	-	G.gal
*Takifugu rubripes*	-	-	-	-	-	-	-	-	-	T.rub
*Tetraodon nigroviridis*	-	-	-	-	-	-	-	-	-	YES (on T.nig)	T.nig
*Ciona intestinalis*	-	-	-	-	-	-	-	-	-	-	-	C.int
*Ciona savignyi*	-	-	-	-	-	-	-	-	-	-	-	YES (on C.int)	C.sav
*Dasypus novemcinctus*	YES (on D.nov)	-	-	-	-	-	-	-	-	-	-	-	-	D.nov
*Echinops telfairi*	YES (on E.tel)	-	-	-	-	-	-	-	-	-	-	-	-	-	E.tel
*Loxodonta africana*	YES (on L.afr)	-	-	-	-	-	-	-	-	-	-	-	-	-	-	L.afr
*Oryctolagus cuniculus*	YES (on O.cun)	-	-	-	-	-	-	-	-	-	-	-	-	-	-	-	O.cun

Translated Blat Analysis

Translated blat (Kent W, Genome Res., 2002;12(4):656-64) is used to look for homologous regions between more distantly related pairs of species. We expect to find homologies mainly in coding regions.

	H.sap	M.mus	R.nor	G.gal	X.tro	D.rer	T.rub	T.nig	C.int	C.sav	A.aeg	D.mel	A.gam
*Homo sapiens*	H.sap
*Mus musculus*	-	M.mus
*Rattus norvegicus*	-	-	R.nor
*Gallus gallus*	YES	YES	YES	G.gal
*Xenopus tropicalis*	YES	YES	-	YES	X.tro
*Danio rerio*	YES	YES	YES	YES	YES	D.rer
*Takifugu rubripes*	YES	YES	-	-	-	YES	T.rub
*Tetraodon nigroviridis*	YES	YES	YES	YES	YES	YES	-	T.nig
*Ciona intestinalis*	YES	-	-	YES	-	YES	-	-	C.int
*Ciona savignyi*	YES	-	-	YES	-	YES	-	-	-	C.sav
*Aedes aegypti*	-	-	-	-	-	-	-	-	-	-	A.aeg
*Drosophila melanogaster*	-	-	-	-	-	-	-	-	-	-	YES	D.mel
*Anopheles gambiae*	-	-	-	-	-	-	-	-	-	-	YES	YES	A.gam

MLAGAN Analysis

Mlagan (Brudno M et al., Genome Res., 2003;13(4):721-31) is used to provide global multiple genomic alignments. First, Mercator is used to build a synteny map between the genomes and then Mlagan builds alignments in the syntenic regions.

3 primates MLAGAN

Homo sapiens
Pan troglodytes
Macaca mulatta

5 eutherian mammals MLAGAN

Mus musculus
Homo sapiens
Rattus norvegicus
Bos taurus
Canis familiaris

7 amniota vertebrates MLAGAN

Mus musculus
Homo sapiens
Gallus gallus
Monodelphis domestica
Rattus norvegicus
Bos taurus
Canis familiaris

Protein Homology Analysis

Three types of homology relationships are provided.

Protein trees are calculated using the longest peptide of all the Ensembl protein coding genes. Proteins are clustered based on Best-Reciprocal Hits and Blast Score Ratios. Each cluster of protein is aligned using Muscle. PHYML is used to get a gene tree from each multiple alignment. The gene tree is reconciliated with the species tree using RAP to root the tree and to call duplication events.

Homologues (orthologues and paralogues) are deduced from the protein trees. A more detailed description of the method is provided here

Families are groups of related genes. The full set of Ensembl proteins is extended using all the metazoan proteins from SwissProt and SPTrEMBL.

Ashbya Genome Database .