I have a large list of genomic positions for the latest assembly of the rat genome (rn4). I would like to map those positions onto the genome and get a list of protein coding genes that lie in the same regions.
More specifically, my questions are:
I understand that the Rat Genome Sequencing Consortium (http://www.hgsc.bcm.tmc.edu/project-species-m-Rat.hgsc?pageLocation=Rat) provides the reference assembly for the rat genome. How does the annotated data available at UCSC Genome Browser, NCBI Genome and ENSEMBL compare and what kind of annotation do they offer?
Which database would you use for the task described above (return genes for genomic positions)?
What program would you use to do that (e.g. R/BioConductor ...)?
I haven't worked much with sequence data before and I am a little confused with the diversity of annotation databases. Any help would be great!