Calign: aligning sequences with restricted affine gap penalties

Motivation: Given a genomic DNA sequence, it is still an open problem to determine its coding regions, i.e. the region consisting of exons and introns. The comparison of cDNA and genomic DNA helps the understanding of coding regions. For such an application, it might be adequate to use the restricted affine gap penalties which penalize long gaps with a constant penalty. Results: Several techniques developed for solving the approximate string-matching problem are employed to yield efficient algorithms for computing the optimal alignment with restricted affine gap penalties. In particular, efficient algorithms can be derived based on the suffix automaton with failure transitions an on the diagonalwise monotonicity of the cost tables. We have implemented the above methods in C on Sun workstations running SunOS Unix. Preliminary experiments show that these approaches are very promising for aligning a cDNA sequence with a genomic DNA sequence.