title: ALP & FALP: C++ libraries for pairwise local alignment E-values.
abstract: BACKGROUND
  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.
  
  
  METHODS
  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.
  
  
  BACKGROUND
  spouge@nih.gov
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, MD 20894, USA and.
authors.forename: Sergey
authors.initials: S
authors.lastname: Sheetlin
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, MD 20894, USA and.
authors.forename: Yonil
authors.initials: Y
authors.lastname: Park
authors.affiliation: Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology, Koto-ku, Tokyo 135-0064, Japan.
authors.forename: Martin C
authors.initials: MC
authors.lastname: Frith
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, MD 20894, USA and.
authors.forename: John L
authors.initials: JL
authors.lastname: Spouge
mesh_terms: D019295:Computational Biology / Q000379:methods*; D004247:DNA / Q000737:chemistry* / Q000378:metabolism; D016208:Databases, Factual; D006801:Humans; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software
chemical_list: D011506:Proteins; D004247:DNA