[BioC] get position information for different gene/transcript IDs

shirley zhang shirley0818 at gmail.com
Wed Aug 18 04:26:49 CEST 2010

Dear list,

I have a list of human SNPs and genes/transcripts which are obtained
from different studies.  I would like to calculate the distance
between these SNPs and genes/transcripts on the same chromosome.
However, the ID for the gene/transcript across studies  is not
consistent. For example, the ID could be Gene Symbol/Alias (TRIM5l),
RNA nucleotide accession (NM_013387), XM_173221 (its gene symbol is
LOC254266, but its record is an obsolete version), Contig22780_RC,
HSS00001378, Hs.445401 (UniGene entry Hs.445401), etc.

I would like to retrieve the start and end position for those
gene/transcript. Can anybody help me how to get the position
information based on these different gene/transcript IDs. If I also
need to match all of other IDs to gene symbol/entrezID, what kind of
database or bioConductor package will allow me to do the mapping as
perfect as possible? How about biomaRt package?


More information about the Bioconductor mailing list