I was wondering if anyone has used the Spaln program (https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3488211/ and http://www.genome.ist.i.kyoto-u.ac.jp/~aln_user/spaln/) to map and align cDNA and EST sequences to the genome. I am particularly interested in understanding the Spaln behaviour on soft-masked genomic sequences. Is the behavior similar to BLAT, where the seeding phase avoids the soft-masked regions but the extension phase does not? or does it behave similar to GMAP which does not care for lowercase or uppercase characters. Any information would help a lot.