POME is a Poisson mixed-effects (or in short, model to characterize base-level read coverage within each transcript. The underlying expression level is included as a key parameter in this model. Because the proposed model is capable of incorporating base-specific variation as well as between-base dependence that affect read coverage profile throughout the transcript, it can lead to improved quantification of the true underlying expression level.
POME can be freely downloaded at http://www.stat.purdue.edu/~yuzhu/pome.html
- Hu M, Zhu Y, Taylor JM, Liu JS, Qin Z. (2011) Using Poisson mixed-effects model to quantify transcript-level gene expression in RNA-Seq. Bioinformatics [Epub ahead of print]. [abstract]