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?
3 answers
Use gmap. It was build for that and outputs a gff file with each exon of every sequence in input. Very usefull !
Aligners do not really have the concept of a gene, only transcript. If you want to treat each transcript as a gene, that can be done pretty easily by adding a tag to the resulting GFF annotation column in a post-alignment step.
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Sean Davis
I never had to solve this problem myself but I am guessing that a long read aligner such as lastz executed with smaller (zero?) penalty for gap extension might work.
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Istvan Albert
Have you tried blastx to compare against protein databases and then backtrack to the genes from the top protein hit? That could solve your problem with minimal human intervention, if you script the efetch to get gene from protein identifier. Exon junctions can then be an SQL query to UCSC Genome Browser.
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