The paper addresses the problem of how to use RNA-Seq data for transcriptome 
reconstruction and quantification, as well as novel transcript discovery in 
partially annotated genomes. We present a novel annotation-guided general 
framework for transcriptome discovery, reconstruction and quantification in 
partially annotated genomes and compare it with existing annotation-guided and 
genome-guided transcriptome assembly methods. Our method, referred as Discovery 
and Reconstruction of Unannotated Transcripts (DRUT), can be used to enhance 
existing transcriptome assemblers, such as Cufflinks, as well as to accurately 
estimate the transcript frequencies. Empirical analysis on synthetic datasets 
confirms that Cufflinks enhanced by DRUT has superior quality of reconstruction 
and frequency estimation of transcripts.