Thanks for quick answer. On Fri, Jun 26, 2009 at 6:49 PM, Katrina Learned <[email protected]>wrote:
> 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 >> >> > -- Sincerely Yours, Alexandra Rapoport _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
