ALP & FALP: C++ libraries for pairwise local alignment E-values
By Sergey Sheetlin, Yonil Park, Martin C. Frith, J. Spouge. 2015
7 citations recorded by the source corpus.
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.
Subfields: Materials Chemistry, Molecular Biology
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Citations in the corpus
- Clustering huge protein sequence sets in linear time (2017, methodology): “cording to the gap-corrected Karlin-Altschul statistics using the ALP library [33]; (2) a minimum coverage (option -c [0,1], which is defined by the number of aligned residue pairs divided by either the maximum of the length of query/centre and target/non-centre sequences (default mode, --cov-mode 0”