Sergey Sheetlin1, Yonil Park1, Martin C Frith2, John L Spouge1. 1. National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, MD 20894, USA and. 2. Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan.
Abstract
MOTIVATION: 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. AVAILABILITY AND IMPLEMENTATION: 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 FALP. CONTACT: spouge@nih.gov SUPPLEMENTARY 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.
MOTIVATION: 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. AVAILABILITY AND IMPLEMENTATION: 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 FALP. CONTACT: spouge@nih.gov SUPPLEMENTARY 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.