Autarchy of the Private Cave » HomoloGene https://bogdan.org.ua Tiny bits of bioinformatics, [web-]programming etc Wed, 28 Dec 2022 16:09:04 +0000 en-US hourly 1 https://wordpress.org/?v=3.8.27 Batch-retrieve EntrezGene homologs using NCBI’s HomoloGene and R’s annotationToolshttps://bogdan.org.ua/2010/10/27/batch-retrieve-entrezgene-homologs-using-ncbi-homologene-and-r.html https://bogdan.org.ua/2010/10/27/batch-retrieve-entrezgene-homologs-using-ncbi-homologene-and-r.html#comments Wed, 27 Oct 2010 10:49:01 +0000 http://bogdan.org.ua/?p=1168
  • Install the annotationTools R package:
    source(“http://bioconductor.org/biocLite.R”)
    biocLite(“annotationTools”)
  • Download full HomoloGene data file from ftp://ftp.ncbi.nlm.nih.gov/pub/HomoloGene/current
  • library(annotationTools)
  • 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.

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