I would like to retrieve the gene structure of as many genes as possible for a specific group of organisms. None of the species of interest have their genome sequenced,
After sequencing the genome you can use a GENE PREDICTION TOOL, like Augustus (http://augustus.gobics.de/). If there is a closely related specie which genome were sequenced you can try to align it using BLAT, or other alignment tool, and retrieve the structure of the homolog genes.
Hi Jordi,
Can you give some more information? What kind of data do you have? RNA-Seq, DNA-Seq?
EMBOSS tool can predict it and after you will need a bit of programming to extract the information i think
Use Augustus (http://bioinf.uni-greifswald.de/augustus/submission/) for closely related species (run it for several to be on the safe side). From the Augustus output it will be easy to extract the introns/exons with a simple script, because all the coordinates are reported; besides, you get the cDNA and the predicted proteins. I don't think you will need any Blasting after that.
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