Gene name assignment/ Merge genome-based assembled transcripts with de novo transcrip

[htk]

Dear all,

I am planninng to build a transcriptome database of a chicken cell line from RNA-seq data. The genome information is available, but it lacks not a few number of gene sequence information. Thus, I'd like to integrate genome-based assembly with de novo assembly. The two data are isoform-aware.

Here, I have two questions;
1.Are there any good tools available to merge two set of transcriptome data, generated from genome-based assembly and de novo assembly?
2.How to assign gene names to the de novo assembled transcripts?

Thanks in advance for your help!