From: Charles Plessy Date: Fri, 1 Jul 2022 06:24:54 +0000 (+0900) Subject: Syntenic correlation indices. X-Git-Url: https://source.charles.plessy.org/?a=commitdiff_plain;h=78408e6d14f2f62ea1c3e17389f1bf48b0d153d2;p=setup%2F.git Syntenic correlation indices. --- diff --git a/biblio/12242252.mdwn b/biblio/12242252.mdwn new file mode 100644 index 00000000..54eebb3e --- /dev/null +++ b/biblio/12242252.mdwn @@ -0,0 +1,23 @@ +[[!meta title="Measures of synteny conservation between species pairs."]] +[[!tag synteny method]] + +Housworth EA, Postlethwait J + +Genetics. 2002 Sep;162(1):441-8. doi:10.1093/genetics/162.1.441 + +Measures of synteny conservation between species pairs. + +[[!pmid 12242252 desc="Introduces a syntenic correlation measure, ρ, which is a +scaled chi-square statistic, and an alternative measure λ with measures “the +proportion of errors made in assigning a gene to a chromosome in one species +that can be eliminated by knowing which chromosome the orthologue belongs to in +the other species.”"]] + +“_We introduce a measure of genomic conservation, which we call syntenic +correlation, which corresponds to a measure of how far the orthologues are from +being independently scattered in the genomes of the two species. This measure +is standardized to be between zero, for completely randomized arrangements of +orthologues between the genomes, and one, for two genomes with perfect synteny +conservation. Further, this measure can be used to compare genomic distances +(i.e., Oxford grids) between many pairs of species._” + diff --git a/tags/synteny.mdwn b/tags/synteny.mdwn index 9fee169a..1535701c 100644 --- a/tags/synteny.mdwn +++ b/tags/synteny.mdwn @@ -84,6 +84,12 @@ Squid chromosomes still have synteny with scallop, but gene order is scrambled orthologue co-occurs close by in the other genome. It varies between 0 (no co-occurrence) and 1 (complete gene order conservation)”. + - [[Housworth and Postlethwait, 2002|biblio/12242252]] defined the syntenic + correlation measure ρ, based on chi-square and an alternative λ not based on + chi-square. Both attempt to estimate how wrong we would be to hypothesise + that a given gene has its orthologue in a homologous chromosome of a related + species. + - “Chains” and “nets” of pairwise alignements between two genomes are described in [[Kent and coll, 2003|biblio/14500911]].