Patent ID: 7089121

Claim:
A computer-implemented method for analyzing the expression of splice variants comprising: a. Selecting a plurality of transcripts of a gene from sequence databases; b. Aligning a sequence of said transcripts to a corresponding genomic sequence; c. Identifying gene features from at least one part of said transcripts aligned with the corresponding genomic sequence; d. Selecting oligonucleotides probes targeting said gene features; e. Hybridizing a target nucleic acid to an array of said oligonucleotide probes; f. Obtaining a plurality of probe intensities, wherein the probe intensities indicates the level of the hybridization of nucleic acid probes with various gene structures wherein the structures identify each splice variant; g. Analyzing the probe intensities across multiple experiments with a model-based algorithm wherein the gene structures are constraints; and h. Estimating the relative concentration of the splice variants with model parameters wherein the model parameters are obtained through a maximum likelihood estimation process.