Hi Lipika, In my previous email, I forgot to mention which table contains this information. The UCSC Genes track has two tables that, together, contain the information you are looking for. The main table, knowGene, contains the chromosome and position, and the kgAlias table contains the RefSeq protein accession (NP-XXXXXX). The two tables are linked by the common field, the known gene ID (knownGene.name & kgAlias.kgID). You can download these tables from our download server here: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/
Katrina Learned UCSC Genome Bioinformatics Group Katrina Learned wrote, On 08/27/10 09:11: > Hi Lipika, > > The data is available in our downloadable tables, however, we don't have > an automated way of providing the the RefSeq ID for a set of > coordinates. You would have to develop code to do retrieve the IDs based > on the chromosome number and genomic position. > > Please don't hesitate to contact the mail list again if you have any > further questions. > > Katrina Learned > UCSC Genome Bioinformatics Group > > > Lipika Ray wrote, On 08/24/10 13:07: > >> Dear UCSC genome broser group, >> >> I have set of genomic position based on hg18, I like to get the >> corresponding refseq accession, like 'NP_XXXXXX' - how can I get that using >> your downloadable tables? >> One example is like this: >> >> Chrom, position, Refseq protein ID >> 1,878522,NP_056473 >> >> So using chromosome number and genomic position, I like to get NP numbers >> based on hg18. >> >> Thanks a lot for any help! >> >> Lipika Ray >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
