This experiment identifies transcription start sites of non-trans-spliced transcripts in C. elegans genomic sequence. Initially, we run genefinder to predict protein-coding transcripts from the C. elegans chromosome sequences. We align existing cDNA and EST sequences to the predicted transcript sequences to confirm the transcript structure. Predicted splice junctions near the 5' transcript end that are unconfirmed by these alignments are tested for confirmation using 5' RACE, DNA sequencing, and sequence alignment. The resulting reads are aligned to the WS170 genomic sequences, the splice leader sequences, and the 5' RACE primer sequence. Combinations of the read-genomic and read-primer alignments are used to identify transcription start sites.