Failed RT-PCR clones for Mammalian Gene Collection $organism C-list from Washington University St. Louis.
This track includes predicted transcripts on which experiments were performed but which failed. Failure can mean either no amplicon was produced or that the amplicon did not 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 FAIL is determined if any one of the following criteria isn't met, 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. The track items consist of the sequence sequenced between the chosen primers.
Updated 2005-05-19
Michael Brent's Computational Genomics Group at Washington University St. Louis.