Technical Report Number
Three methods for analyzing sequencing traces derived from sequencing reactions containing two DNA templates are presented. All rely on alignment to a segment of assembled genomic sequence containing the original template sequence. Spliced alignment algorithms are used so that traces derived from processed mRNA can be analyzed. The main application of these techniques is the elucidation of alternately spliced transcripts. Several experimental verification of one of the techniques is presented including testing on a set of 48 alternately spliced targets from the human genome and 47 negative controls.
Tenney, Aaron, "Basecalling for Traces Derived for Multiple Templates" Report Number: WUCSE-2004-80 (2004). All Computer Science and Engineering Research.