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
