BACKGROUND: mRNA-Seq technology has revolutionized the field of transcriptomics 
for identification and quantification of gene transcripts not only at gene level 
but also at isoform level. Estimating the expression levels of transcript 
isoforms from mRNA-Seq data is a challenging problem due to the presence of 
constitutive exons.
RESULTS: We propose a novel algorithm (IsoformEx) that employs weighted 
non-negative least squares estimation method to estimate the expression levels 
of transcript isoforms. Validations based on in silico simulation of mRNA-Seq 
and qRT-PCR experiments with real mRNA-Seq data showed that IsoformEx could 
accurately estimate transcript expression levels. In comparisons with published 
methods, the transcript expression levels estimated by IsoformEx showed higher 
correlation with known transcript expression levels from simulated mRNA-Seq 
data, and higher agreement with qRT-PCR measurements of specific transcripts for 
real mRNA-Seq data.
CONCLUSIONS: IsoformEx is a fast and accurate algorithm to estimate transcript 
expression levels and gene expression levels, which takes into account short 
exons and alternative exons with a weighting scheme. The software is available 
at http://bioinformatics.wistar.upenn.edu/isoformex.