ALP和FALP：用于成对局部比对E值的C++库。
ALP & FALP: C++ libraries for pairwise local alignment E-values.
作者信息
Sheetlin Sergey, Park Yonil, Frith Martin C, Spouge John L
机构信息
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.
出版信息
Bioinformatics. 2016 Jan 15;32(2):304-5. doi: 10.1093/bioinformatics/btv575. Epub 2015 Oct 1.
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
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
动机
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。
可用性与实现方式
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。
联系方式
补充信息
补充数据可在《生物信息学》在线获取。
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