Patent Document ID: 10055539
Application ID: 14798686
Patent Flag: 1

Claim One:
1. A system for analyzing a transcriptome, the system comprising: a processor coupled to the memory, wherein the system is operable to: obtain, from an annotated transcriptome database, a plurality of exons and introns from a genome; use the processor to transform the plurality of exons and introns into a directed acyclic data structure comprising nodes representing known RNA sequences and edges connecting the nodes; obtain a pair of paired-end reads generated by sequencing a transcriptome of an organism; use the processor to transform the first read of the pair into an alignment with an optimal score between that first read of the pair and a node in the directed acyclic data structure; identify, using the processor, candidate paths within the directed acyclic data structure that include the node connected to a downstream node by a path having a length substantially similar to an insert length of the pair of paired-end reads; exclude non-candidate paths from alignments involving the pair of paired-end reads; align, using the processor, the paired-end reads to the candidate paths to determine an optimal-scoring alignment by: calculating match scores between a second read of the pair and nodes in the candidate paths, and looking backwards to predecessor nodes in the candidate paths while not considering any nodes in the non-candidate paths to identify a back-trace through the candidate paths that gives an optimal score, wherein the back-trace that gives the optimal score corresponds to an optimal scoring alignment of the pair of paired-end reads to the candidate paths, and wherein the directed acyclic data structure held in the memory prior to obtaining the pair of paired-end reads includes at least one path that has a node that the second read of the pair aligns to but that is not included during the aligning step due to being excluded as a noncandidate path; and identify an isoform of an RNA from the organism using the optimal scoring alignment of the paired-end reads.