Hi All, The explanation supplied is not adequate. The RefSeq project supplies information on transcripts that are unique - and on the NCBI (which created refseq), indeed, there is only ONE record per acession. (Try a simple search in Entrez). Indeed, the refseq project often supplies muliple accession for the same or similar loci with various splices. That's the whole point. It's a conservative approach - one name, one transcript. There is a mistake in the adaptation of their database to yours. Your explanation makes no sense unless you went and did all the alignments and selection from scratch - and if that's the case, why would you call it a RefSeq track?
maayan On Thu, Nov 25, 2010 at 12:08 AM, Pauline Fujita <[email protected]>wrote: > Hello Maayan, > > Please see this previously answered mailing list question about the same > issue: > > https://lists.soe.ucsc.edu/pipermail/genome/2010-November/024242.html > > Hopefully this information was helpful and answers your question. If you > have further questions or require clarification feel free to contact the > mailing list at [email protected]. > > Regards, > > Pauline Fujita > UCSC Genome Bioinformatics Group > http://genome.ucsc.edu > > > > On 11/24/10 01:08, maayan kreitzman wrote: > >> Hi there, >> I've found a kind of serious problem with your database which is based on >> the RefSeq project. >> Many of the refseq accessions, when queried from the genome browser return >> more than one gene, IN COMPLETELY DIFFERENT LOCATIONS. >> If you search, say, NM_198181, this is the case. Sometimes, like in the >> case >> of NM_020364, the different entries are even on opposite strands. >> if you want a longer list of examples like this, I can send you some more. >> The mistake is somewhere in the conversion from the RefSeq database to >> your >> software, because if you search the same accessions in Entrez you get, as >> expected, ONE gene. >> Reqseq documents specific, unique, verified transcripts. There should not >> be >> more than one set of coordinates for each refseq accession. >> maayan >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
