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SIBsim4 - high-performance alignment of cDNAs to genomes

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

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