this process.m generates the following files for the current genome
(check process.m)
 
confirmed_sequences.mat					EST & cDNA derived splicegraphs
confirmed_sequences_transform.mat		EST & cDNA derived splicegraphs
										(transformed to local coordinates)

annotation_sequences.mat				genome annotation splicegraphs
annotation_sequences_transform.mat		genome annotation splicegraphs
										(transformed to local coordinates)

confirmed_sequences_split.mat			splitting indexes into several sets
