Successful RT-PCR clones for Mammalian Gene Collection $organism C-list from Washington University St. Louis.
This track includes experimental sequences that splice align to the genomic region of the intended target structure. Est2Genome is used for alignment. Generally parameters are set such that splice_penalty=15, intron_penalty=30, mismatch=3, minscore=20, and gap_penalty=4. A HIT is determined if the alignment has at least one splice, has an overall identity over 75%, at least 60% of the segments in the alignment have 80% identity to the genome, and the terminal exons are at least length 10. A HIT can come from the assembled read or from either the forward or reverse trace. Note that intron novelty is not a criteria for a HIT and that mispriming may be present.
Updated 2005-02-28
Michael Brent's Computational Genomics Group at Washington University St. Louis.