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%A A. Konagurthu
%A L. Allison
%A T. Conway
%A B. Beresford-Smith
%A J. Zobel
%T Design of an efficient out-of-core read alignment algorithm
%I SpringerVerlag
%V 6293
%P 189-201
%D 2010
%K wShop, MolBio, c2010, c201x, c20xx, zz1010, WABI, WABI10, nicta, LAllison,
   Syzygy, ArunK, Algorithms in Bioinformatics, short read, reads, NGS, align,
   mapping, next generation, DNA, sequencing, algorithm
%X "New genome sequencing technologies are poised to enter the sequencing
   landscape with significantly higher throughput of read data produced at
   unprecedented speeds & lower costs per run. However, current in-memory
   methods to align a set of reads to one or more reference genomes are
   ill-equipped to handle the expected growth of read-throughput from newer
   technologies.  ... reports the design of a new out-of-core read mapping alg.,
   Syzygy, which can scale to large volumes of read & genome data. The alg. is
   designed to run in a constant, user-stipulated amount of main memory -
   small enough to fit on standard desktops - irrespective of the sizes of read
   & genome data. Syzygy achieves a superior spatial locality-of-reference that
   allows all large data structures used in the alg. to be maintained on disk.
   We compare our prototype implementation with several popular read alignment
   programs.  Our results demonstrate clearly that Syzygy can scale to very
   large read volumes while using only a fraction of memory in comparison,
   without sacrificing performance."
   -- [more],
   (In: uk us isbn:3642152937; uk us isbn13:978-3-642-15293-1.)

%A S. T. S. Ho
%A L. Allison
%A C. N. Yee
%A T. I. Dix
%T Constraint checking for restriction site mapping
%J 24th Hawaii Int. Conf. on Sys. Sci.
%V ?
%P ???-???
%D 1991
%O TR 89/129 Computer Science, Monash University, JUL '89
%K LAllison, Monash, conf, MolBio, HICSS, HICSS24, HICSS91, bioinformatics,
   restriction site mapping, RSM, map, constraint satisfaction problem CSP,
   separation theory, TR 89/129 89 129 TR89/129 TR129, c1991, c199x, c19xx
%X also see [mapping].

%A S. Ho
%A L. Allison
%A C. N. Yee
%T Restriction site mapping for three or more enzymes
%J Comp. Appl. BioSci. (J. Bioinformatics)
%V 6
%N 3
%P 195-204
%D 1990
%O TR 88/117 Dept. Comp. Sci., Monash University Oct '88
%K LAllison, Monash, jrnl, MolBio, CABIOS, RSM, restriction site map, mapping,
   constraint satisfaction problem, programming, three, separation theory,
   TR 88 117 TR117 TR88/117, c1990, c199x, c19xx, J. Bioinformatics, enzyme
%X "Restriction site mapping requires a generator to put forward possible maps &
   a constraint checker to reject false maps. Ideally these combine to give an
   algorithm which calculates a sound & complete solution set. 3 algorithms for
   generation are presented & compared. Two decompose a multi-enzyme problem
   (3+) into subproblems. The constraint checker is based on separation theory.
   Some insights into the extent of constraint checking involved in & the
   feasibility of more checking for three or more enzymes are discussed. The
   trade-off between comp'n time & the soundness of the soln set is examined."
   [now J. Bioinformatics]
   -- [doi:10.1093/bioinformatics/6.3.195],
   Also see [mapping].

%A L. Allison
%A C. Y. Yee
%T Restriction site mapping is in separation theory
%J Comp. Appl. BioSci. (J. Bioinformatics)
%V 4
%N 1
%P 97-101
%D 1988
%K LAllison, Monash, jrnl, CABIOS, plasmid, map, maps, mapping, combinatorial,
   enzyme, restriction site, DNA, phage, RSM, MolBio, separation theory,
   linear, constraint, programming, algorithm, inequality, c1988, c198x, c19xx,
   J. Bioinformatics, NAR, Nucl. Acids Res. special issue
%X Paper examines constraint checking during backtracking generation
   of solutions to the plasmid mapping problem.
   The constraints fall into Vaughn Pratt's separation theory.
   It is necessary and sufficient to check all simple cycles
   in the graph of restriction sites linked by fragments
   from the two single digests and the one double digest (can be generalized
   to more than two enzymes).
   In general, at level 'n' there are at most n new constraints to check.
      As an efficiency matter, only those cycles containing 1, 2 or 3
   indivisible cycles can be checked which allows a very few false maps to
   be generated.  This reduces total constraints/map from n*n to 3*n.
   -- [more],
      [paper (HTML)],
      [paper (.ps)].
   [jrnl is now  J. Bioinformatics].

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