Sheetlin Sergey, Park Yonil, Frith Martin C, Spouge John L
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, MD 20894, USA and.
Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan.
Bioinformatics. 2016 Jan 15;32(2):304-5. doi: 10.1093/bioinformatics/btv575. Epub 2015 Oct 1.
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 FALP.
Supplementary data are available at Bioinformatics online.
两两局部比对是分子生物学家不可或缺的工具。ALP（升序阶梯程序）能在实时（即约1秒内）针对随机序列的蛋白质-蛋白质或DNA-DNA局部比对，计算任意替换得分矩阵、空位成本和字母丰度下的E值；而FALP（移码升序阶梯程序）虽速度较慢，但能针对移码DNA-蛋白质比对执行类似任务。
为使其他C++程序员能在自己的程序中直接实现ALP和FALP的计算效率，C++源代码可在公共领域通过http://go.usa.gov/3GTSW下的“ALP”和“FALP”获取，同时还有独立程序ALP和FALP。
补充数据可在《生物信息学》在线获取。
