<p>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.</p>

<p>Any suggestions on how to map such sequences to a genome with reliable information about the exon/intron junctions?</p>

<p>Use gmap. It was build for that and outputs a gff file with each exon of every sequence in input. Very usefull !</p>
