PAVE v3.0 provides a unified platform for annotating and analyzing EST transcript data from both current and older sources, e.g. Illumina, 454, and Sanger. The platform has the capability to merge two or more assemblies (preserving the expression levels), allowing existing data to be combined with data generated by newer methods. De Novo assemblies of smaller datasets, e.g. from 454 sequencing, are also supported. The annotation pipeline allows annotation by any number of reference databases. To view and analyze the results, a full-featured browser and query system is also provided, supporting a full range of queries by annotation, differential expression, and other parameters of interest. In addition, transcripts may be automatically compared to all other transcripts to identify gene families or alternately spliced isomers.