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

27th October 2010

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.

This entry was posted on Wednesday, October 27th, 2010 at 12:49 and is filed under Bioinformatics, how-to, Notepad. You can follow any responses to this entry through the RSS 2.0 feed. You can skip to the end and leave a response. Pinging is currently not allowed.

2 Responses to “Batch-retrieve EntrezGene homologs using NCBI’s HomoloGene and R’s annotationTools”

1. Yvan Says:
   March 28th, 2011 at 16:48

   Hello,

   Any idea on how to retrieve full homologenes (with multiple species) using several genebank IDs as input?

   Best regards,

   Yvan

2. Orthology detection | m's Bioinformatics Says:
   December 18th, 2013 at 6:32

   […] Batch-retrieval via R’s annotationTools […]

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