Isoform quantification using RNA-seq

[vinay052003]

I have RNA-seq data from 454 sequencing technology and I want to quantify the expression levels of the splice variants. The first choice available is Cufflinks but that works only for short reads such as from Illumina.
I was going through their algorithm and it sounds a bit complicated to implement. Has anyone done that before? Any suggestions for another program/algorithm for long RNA-seq reads?

Thanks.