I have a set of cDNA-sequences representing mRNAs and I want to create a gtf/gff file of these. I have tried to use BLAST and BLAT, but I find it difficult to obtain a single reliabe hit that represents all the different exons. And especially with BLAT I get many small hits for each sequence. I also tried to map the sequences using TopHat, but for some reason it crashed, perhaps due to the long sequences.
Any suggestions on how to map such sequences to a genome with reliable information about the exon/intron junctions?