How were ESTs aligned?
We aligned the consensus EST sequences of Glycine max, Medicago trunculata and Lotus japonicus from the TIGR Plantta database to the soybean genome using Jim Kent’s BLAT and filtered for best hit to the genome, along with any hit within 97% coverage of that hit to account for genome duplication. For final gene verification we aligned G. max ESTs using Brian Haas’s PASA pipeline which aligns ESTs to the best place in the genome via gmap, then filters hits to ensure proper splice boundaries.
