An Algorithm for Classification of Alternative Splicing and Transcriptional Initiation and Its Genome-Wide Application

This is the authors' abstract. We don't add key points for this paper.

We developed an algorithm that classi es all observed units of alternative splicing and transcriptionalinitiation and termination (UASTs) into an extendable set of distinct elementary patterns, when acollection of alignments between genomic DNA sequences and a set of cDNA/EST sequences are pro-vided. Thealgorithm rstconverts aligned exon-intron structuresinto bitarrays, extracts UASTs, andthen encodes each UAST into a pair (or vector) of decimal numbers, which specify the correspondingpattern. This system can uniquely and compactly encode not only typical patterns but also any rareor novel patterns which have usually been collectively assigned as . This system deals withtranscriptional variation and alternative splicing in the same framework of classi cation.