27th October 2010
- Install the annotationTools R package:
- Download full HomoloGene data file from ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/current
- homologene = read.delim(“homologene.data”, header=FALSE)
- mygenes = read.table(“file with one entrez ID of the source organism per line.txt”)
- 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.