Arabidopsis thaliana gene model alignmentsSequences were aligned to the Physomitrella patens genome using the CAT program (Li et al. 2007) with default parameters and similarity matrix.To remove poor quality alignments a number of filters were applied: 1) alignment segments with a negative CAT value for matched bases were removed, 2) Alignments with an overall alignment percentage below 30% were removed (overall% =percent match ID * percent match length), 3) Where sequences mapped to multiple locations, only alignments 70% similar to the match with the best overall% were retained, 4) alignment segments separated by >3Kb were evaluated as distinct groups with only the alignment part with the highest overall% retained. |