SIBsim4 is based on sim4, which is a program designed to align a cDNA sequence with a genomic sequence, allowing for proper placement of intron/exon junctions. Sim4 was written by Liliana Florea while working in Webb Miller's lab at Pennsylvania State University.
SIBsim4 is a fairly extensive rewrite of the original code with the following goals:
· speed improvement
· allow large, chromosome scale, DNA sequences to be used
· provide more detailed output about splice types
· provide more detailed output about polyA sites
· miscellaneous code cleanups and bug fixes