Hi Alexandra, One of our developers contacted me and explained the reverse strand coordinates much more clearly. Here is what she said:
Genomic coordinates that we store and display are always relative to the positive strand of the reference genome. We reverse-complement genomic sequence when a gene is on the reverse strand, but genomic coordinates are still forward. So for a gene on the reverse strand, txStart is its 3' end, txEnd is its 5' end, and the exon coordinates are listed 3' to 5' (backwards). I hope this is helpful! Please don't hesitate to contact the mail list again if you require further assistance. Katrina Learned UCSC Genome Bioinformatics Group Katrina Learned wrote: > Hi Alexandra, > > Yes, in the case of a gene on the negative strand, the sequence returned > by the Table Browser (I think this is the tool you are using, if not, > please let me know) will be relative to that gene, or, in other words, > the reverse complement of the genomic DNA. > > You should use the txStart and txEnd fields as your coordinates > regardless of which strand you are using. Even when your gene of > interest is on the reverse strand, your txStart will always be a lower > number (coordinate) than your txEnd because the Table Browser provides > information in accordance with the direction the gene is transcribed. > > Please don't hesitate to contact the mail list again if you require > further assistance. > > Katrina Learned > UCSC Genome Bioinformatics Group > > > Rapoport Alexandra wrote: > >> Greetings! >> I'm using Your database for retrieving repeat sequences for various >> organisms, during my work two questions arose: >> 1. If I use 'sequence' output option - is the result for '-' strand are >> already reverse complement? >> 2. If I want to retrieve the sequences using chromosome coordinates from >> 'all fields from selected table' output and chr*.fa.gz file downloaded from >> Your site, what coordinates should I use for reverse string? >> I performed a search in the mailing list, but, unfortunately, did not >> succeed to find the answers >> Thanks in advance >> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
