Pairwise local alignment is an indispensable tool for molecular biologists. In real time (i.e. in about 1 s), ALP (Ascending Ladder Program) calculates the E-values for protein-protein or DNA-DNA local alignments of random sequences, for arbitrary substitution score matrix, gap costs and letter abundances; and FALP (Frameshift Ascending Ladder Program) performs a similar task, although more slowly, for frameshifting DNA-protein alignments.To permit other C++ programmers to implement the computational efficiencies in ALP and FALP directly within their own programs, C++ source codes are available in the public domain at http://go.usa.gov/3GTSW under 'ALP' and 'FALP', along with the standalone programs ALP and [email protected] information: Supplementary data are available at Bioinformatics online. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.
Journal: Bioinformatics
DOI: 10.1093/bioinformatics/btv575
Year: 2016