454 and Illumina data; classifying reads/contigs

[poisson200]

Dear All,
Does anyone know of a good program for classifying reads as;

1) intergenic
2) exonic
3) intronic
4) intagenic

For the 454 data, I have clustered reads using Roche's newbler assembly program and I have tried using cd-hit-est to cluster reads with Refseq transcriptome, thinking reads with alternative exons will not cluster. This is the case but I get too many contigs that have a few SNPs that also don't cluster; so the process is not quick.

Software for classifying Illumina reads would also be cool.

Any advice appreciated. Thanks.

Thanks,

John.