rae230aREFSEQ {rae230a}R Documentation

Mappings between probe identifiers and RefSeq identifiers

Description

The Reference Sequence (RefSeq) database contains curated non-redundant set of sequences for genomic DNA, RNA, and protein for various organisms. rae230aREFSEQ maps probe identifiers to all the RefSeq identifiers that are mapped by NCBI to genes represented by the probe identifiers

Details

RefSeq ids differ in format according to the type of record the ids are for as shown below:

NG_XXXXX: RefSeq accessions for genomic region (nucleotide) records

NM_XXXXX: RefSeq accessions for mRNA records

NC_XXXXX: RefSeq accessions for chromosome records

NP_XXXXX: RefSeq accessions for protein records

XR_XXXXX: RefSeq accessions for model RNAs that are not associated with protein products

XM_XXXXX: RefSeq accessions for model mRNA records

XP_XXXXX: RefSeq accessions for model protein records

Where XXXXX is a sequence of integers.

NCBI http://www.ncbi.nlm.nih.gov/RefSeq/ allows users to query the RefSeq database using RefSeq ids.

Mappings were based on data provided by:

LocusLink:ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz. Built: September 15, 2004

Package built Thu Sep 16 09:31:44 2004

References

NCBI http://www.ncbi.nlm.nih.gov and RefSeQ http://www.ncbi.nlm.nih.gov/RefSeq/

Examples

    # Convert the environment to a list
    xx <- as.list(rae230aREFSEQ)
    # Remove probe ids that do not map to any RefSeq
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
    # The RefSeq for the first two elements of XX
    xx[1:2]
    # Get the first one
    xx[[1]]
}

[Package rae230a version 1.6.5 Index]