Convert gene IDs between different species

http://bogdan.org.ua/2010/10/27/batch-retrieve-entrezgene-homologs-using-ncbi-homologene-and-r.html

1. Install the annotationTools R package:
source(“http://bioconductor.org/biocLite.R”)
biocLite(“annotationTools”)
2. Download full HomoloGene data file from ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/current
3. library(annotationTools)
4. homologene = read.delim(“homologene.data”, header=FALSE)
5. mygenes = read.table(“file with one entrez ID of the source organism per line.txt”)
6. getHOMOLOG(unlist(mygenes), taxonomy_ID_of_target_organism, homologene) [alternatively, wrap the call to getHOMOLOG into unlist to get a vector]


##get mouse (species ID 10090) orthologs of several human (species ID 9606)