Batch-retrieve EntrezGene homologs using NCBI’s HomoloGene and R’s annotationTools

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]

It might be easier to achieve the same results with a Perl script calling NCBI’s e-utils.