Results 1 - 10 of 21,648

Multiple sequence alignment with the Clustal series of programs

by Ramu Chenna, Hideaki Sugawara, Tadashi Koike, Rodrigo Lopez, Toby J. Gibson, Desmond G. Higgins, Julie D. Thompson - Nucleic Acids Res , 2003
"... The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also the ..."
Abstract - Cited by 747 (5 self) - Add to MetaCart
The Clustal series of programs are widely used in molecular biology for the multiple alignment of both nucleic acid and protein sequences and for preparing phylogenetic trees. The popularity of the programs depends on a number of factors, including not only the accuracy of the results, but also

A semantics of multiple inheritance

by Luca Cardelli - Information and Computation , 1988
"... There are two major ways of structuring data in programming languages. The first and common one, used for example in Pascal, can be said to derive from standard branches of mathematics. Data is organized as cartesian products (i.e. record types), disjoint sums (i.e. unions or variant types) and func ..."
Abstract - Cited by 528 (9 self) - Add to MetaCart
There are two major ways of structuring data in programming languages. The first and common one, used for example in Pascal, can be said to derive from standard branches of mathematics. Data is organized as cartesian products (i.e. record types), disjoint sums (i.e. unions or variant types

Muscle: multiple sequence alignment with high accuracy and high throughput

by Robert C. Edgar - NUCLEIC ACIDS RES , 2004
"... We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the logexpectation score, and refinement using tree-dependent r ..."
Abstract - Cited by 2509 (7 self) - Add to MetaCart
We describe MUSCLE, a new computer program for creating multiple alignments of protein sequences. Elements of the algorithm include fast distance estimation using kmer counting, progressive alignment using a new profile function we call the logexpectation score, and refinement using tree

MAFFT version 5: improvement in accuracy of multiple sequence alignment

by Kazutaka Katoh, Kei-ichi Kuma, Hiroyuki Toh, Takashi Miyata - NUCLEIC ACIDS RES , 2005
"... The accuracy of multiple sequence alignment pro-gram MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed high ..."
Abstract - Cited by 801 (5 self) - Add to MetaCart
The accuracy of multiple sequence alignment pro-gram MAFFT has been improved. The new version (5.3) of MAFFT offers new iterative refinement options, H-INS-i, F-INS-i and G-INS-i, in which pairwise alignment information are incorporated into objective function. These new options of MAFFT showed

Dryad: Distributed Data-Parallel Programs from Sequential Building Blocks

by Michael Isard, Mihai Budiu, Yuan Yu, Andrew Birrell, Dennis Fetterly - In EuroSys , 2007
"... Dryad is a general-purpose distributed execution engine for coarse-grain data-parallel applications. A Dryad applica-tion combines computational “vertices ” with communica-tion “channels ” to form a dataflow graph. Dryad runs the application by executing the vertices of this graph on a set of availa ..."
Abstract - Cited by 762 (27 self) - Add to MetaCart
of available computers, communicating as appropriate through files, TCP pipes, and shared-memory FIFOs. The vertices provided by the application developer are quite simple and are usually written as sequential programs with no thread creation or locking. Concurrency arises from Dryad scheduling vertices to run

Static Scheduling of Synchronous Data Flow Programs for Digital Signal Processing

by Edward Ashford Lee, David G. Messerschmitt - IEEE TRANSACTIONS ON COMPUTERS , 1987
"... Large grain data flow (LGDF) programming is natural and convenient for describing digital signal processing (DSP) systems, but its runtime overhead is costly in real time or cost-sensitive applications. In some situations, designers are not willing to squander computing resources for the sake of pro ..."
Abstract - Cited by 598 (37 self) - Add to MetaCart
special case of Petri nets. This self-contained paper develops the theory necessary to statically schedule SDF programs on single or multiple proces-sors. A class of static (compile time) scheduling algorithms is proven valid, and specific algorithms are given for scheduling SDF systems onto single

A SOUND TYPE SYSTEM FOR SECURE FLOW ANALYSIS

by Dennis Volpano, Geoffrey Smith, Cynthia Irvine , 1996
"... Ensuring secure information ow within programs in the context of multiple sensitivity levels has been widely studied. Especially noteworthy is Denning's work in secure ow analysis and the lattice model [6][7]. Until now, however, the soundness of Denning's analysis has not been established ..."
Abstract - Cited by 540 (21 self) - Add to MetaCart
Ensuring secure information ow within programs in the context of multiple sensitivity levels has been widely studied. Especially noteworthy is Denning's work in secure ow analysis and the lattice model [6][7]. Until now, however, the soundness of Denning's analysis has not been

Implementation and performance of Munin

by John B. Carter, John K. Bennett, Willy Zwaenepoel - IN PROCEEDINGS OF THE 13TH ACM SYMPOSIUM ON OPERATING SYSTEMS PRINCIPLES , 1991
"... Munin is a distributed shared memory (DSM) system that allows shared memory parallel programs to be executed efficiently on distributed memory multiprocessors. Munin is unique among existing DSM systems in its use of multiple consistency protocols and in its use of release consistency. In Munin, sha ..."
Abstract - Cited by 587 (22 self) - Add to MetaCart
Munin is a distributed shared memory (DSM) system that allows shared memory parallel programs to be executed efficiently on distributed memory multiprocessors. Munin is unique among existing DSM systems in its use of multiple consistency protocols and in its use of release consistency. In Munin

AFNI: software for analysis and visualization of functional magnetic resonance neuroimages

by Robert W Cox - Computers and Biomedical Research , 1996
"... email rwcoxmcwedu A package of computer programs for analysis and visualization of threedimensional human brain functional magnetic resonance imaging FMRI results is described The software can color overlay neural activation maps onto higher resolution anatomical scans Slices in each cardinal pl ..."
Abstract - Cited by 807 (3 self) - Add to MetaCart
data sets are described Facilities are provided for several types of statistical analyses of multiple D functional data sets The programs are written in ANSI C and Motif to run on Unix workstations

Hidden Markov models in computational biology: applications to protein modeling

by Anders Krogh, Michael Brown, I. Saira Mian, Kimmen Sjölander, David Haussler - JOURNAL OF MOLECULAR BIOLOGY , 1994
"... Hidden.Markov Models (HMMs) are applied t.0 the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are demonstrated the on globin family, the protein kinase catalytic domain, and the EF-hand calcium binding moti ..."
Abstract - Cited by 655 (39 self) - Add to MetaCart
protein family, or contain the given domain. The Hi " produces multiple alignments of good quality that agree closely with the alignments produced by programs that incorporate three-dimensional structural information. When employed in discrimination tests (by examining how closely the sequences in a
Results 1 - 10 of 21,648