LASSAP, a LArge Scale Sequence Comparison Package.

MOTIVATION:This paper presents LASSAP, a new software package for sequence comparison. LASSAP is a programmable, high-performance system designed to raise current limitations of sequence comparison programs in order to fit the needs of large-scale analysis. LASSAP provides an API (Application Programming Interface) allowing the integration of any generic pairwise-based algorithm.RESULTS:Whatever pairwise algorithm is used in LASSAP, it shares with all other algorithms numerous enhancements such as: (i) intra- and inter-databank comparisons; (ii) computational requests (selections and computations are achieved on the fly); (iii) frame translations on queries and databanks; (iv) structured results allowing easy and powerful post-analysis; (v) performance improvements by parallelization and the driving of specialized hardware. LASSAP currently implements all major sequence comparison algorithms (Fasta, Blast, Smith/Waterman), and other string matching and pattern matching algorithms. LASSAP is both an integrated software for end-users and a framework allowing the integration and the combination of new algorithms. LASSAP is used in different projects such as the building of PRODOM, the exhaustive comparison of yeast sequences, and the subfragments matching problem of TREMBL.