Infers isoforms from short RNA-Seq reads and information concerning exon-intron boundaries and transcription start site (TSS) - poly-A site (PAS) pairs. IsoInfer can calculate the expression levels of isoforms accurately if all the isoforms are known. It can also infer isoforms from scratch when they are sufficiently expressed, by trying to find a minimum set of isoforms to explain the read data. The method works for single-end data and data with both single-end and paired-end read. The software was tested on mouse genes.