Hi Daniel, This is a difficult issue since all of our maf data are kept in files - the data are too large and cumbersome to keep in an easily accessible table that you could access via the publicly available genome-mysql database. One of our engineers had this to say: "I think it might be possible to do this with a sophisticated setup that grabbed byte ranges from the gbdb maf file with offsets from the multizNway table, but it would be a lot of work."
Please feel free to contact the mail list again if you require further assistance. Best, Mary ------------------ Mary Goldman UCSC Bioinformatics Group On 5/17/11 4:57 PM, Daniel Peterson wrote: > Hi, > > I'm looking for a way to retrieve sequence alignments for a specified mRNA > Accession number. I know this is possible via the browser but I would like > to add this ability to a program I am writing. I already found how to get > the exon start and stop locations from the MySql database (hg19), but I > haven't found how to get the sequences from the database. The only way I > have found the sequences was over at > http://hgdownload.cse.ucsc.edu/goldenpath/hg19/multiz46way/alignments/ and > those are huge files, way too big for users of my program to download. > > Is there a way in which I can access the sequence segments which the database > mentions, other than having users download a ~300mb file? > > Daniel Peterson > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
