Dear Madame, dear Sir, I do have a question concerning the Human UCSC gene prediction track. RefSeq and GenBank RNAs are aligned to the genome with BLAT, keeping only the best alignments for each RNA and discarding alignments of less than 98% identity. Imagine a recent gene duplication event, leading to identical alignments at two or multiple locations. Are there unique uc names given for each and every alignment corresponding to each location within the genome or are their identical uc names ascribed to equally good alignments of the same RNA in different positions. If the second scenario is correct, how to identify gene duplications within the UCSC gene prediction set.
Thanks in advance, Carsten _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
