get.similarity.between.genes {KEGGSOAP} | R Documentation |
Given two KEGG ids for genes, the function searches the KEGG GENES database to obtain a measure of the similarity between the two genes. The similarity between genes is determined by alignment of matching bases.
get.similarity.between.genes(genes.id1, genes.id2)
genes.id1 |
genes.id1 a character string for the id used by
KEGG to represent the gene of interest. The id normally consists of
three letters followed by a colon and then several numbers. The
three letters are from the first letter of the genus
name and the first two letters of the species name of the scientific
name of the organism of concern (e. g. hsa:111 for Homo Sapiens) |
genes.id2 |
genes.id2 same as genes.id1 but for
another gene |
The corresponding KEGG SOAP method returns a list of data as described
in the return list of
get.best.neighbors.by.gene
. get.similarity.between.genes
extracts and returns the value for identity from the list.
This function returns a value between 0 and 1 for the protortion of matching bases between the two genes
Jianhua Zhang
http://www.genome.jp/kegg/soap/doc/keggapi_manual.html
if(require("SSOAP") && require("XML")){ get.similarity.between.genes("eco:b0002", "eco:b3940") }