Autarchy of the Private Cave

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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.

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

    1. Yvan Says:

      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:

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

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