Split Refseq Genes Into Coding And Noncoding Genes

Question

[Abhi]

Hi Guys

I would like to divide the refseq hg19 genes into coding and noncoding genes. Is there some annotation available that I can use to bin the genes rather than doing the ORF analysis on them on my own.

Thanks! -Abhi

Answer 1

[Ashutosh Pandey]

You can use this file to get the coding-type information for all human genes: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz There should be a way to use UCSC genome browser directly to get the same information but I am not aware of it.

Answer 2

[Ido Tamir]

look at the name prefix. http://www.ncbi.nlm.nih.gov/books/NBK21091/table/ch18.T.refseq_accession_numbers_and_mole/?report=objectonly Its NM_ vs NR_ where NR are non protein coding. I guess for the bulk it should be o.k. don't know if every instance is correctly classified.