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Subjects / keywords: Computer science; Mathematics; Set theory; Problems, exercises, etc; Algorithms; Logic, Symbolic and mathematical; Problems and exercises; Electronic books

BACKGROUND: Secondary structure forms an important intermediate level of description of nucleic acids that encapsulates the dominating part of the folding energy, is often well conserved in evolution, and is routinely us...

Profile hidden Markov models (profile HMMs) and probabilistic inference methods have made important contributions to the theory of sequence database homology search. However, practical use of profile HMM methods has been...

This paper describes various components of the macromolecular crystallographic refinement program REFMAC5, which is distributed as part of the CCP4 suite. REFMAC5 utilizes different likelihood functions depending on the ...

MOTIVATION: Next-generation sequencing technologies generate very large numbers of short reads. Even with very deep genome coverage, short read lengths cause problems in de novo assemblies. The use of paired-end librarie...

LIBSVM is a library for Support Vector Machines (SVMs). We have been actively developing this package since the year 2000. The goal is to help users to easily apply SVM to their applications. LIBSVM has gained wide popul...

In the Python world, NumPy arrays are the standard representation for numerical data and enable efficient implementation of numerical computations in a high-level language. As this effort shows, NumPy performance can be ...

Subjects / keywords: TREMBLAY, JEAN-PAUL; MCGRAW-HILL; 005.113 T789in

Subjects / keywords: Python (Computer program language); Data structures (Computer science); Computer algorithms

Subjects / keywords: Text processing (Computer science); Genetic algorithms; Computational linguistics

Subjects / keywords: Computer algorithms; Databases; Data structures (Computer science); Structured programming

A key step in mass spectrometry (MS)-based proteomics is the identification of peptides in sequence databases by their fragmentation spectra. Here we describe Andromeda, a novel peptide search engine using a probabilisti...

VESTA is a three-dimensional visualization system for crystallographic studies and electronic state calculations. It has been upgraded to the latest version, VESTA 3 , implementing new features including drawing the exte...

When small RNA is sequenced on current sequencing machines, the resulting reads are usually longer than the RNA and therefore contain parts of the 3' adapter. That adapter must be found and removed error-tolerantly from ...

As with any burgeoning technology that enjoys commercial attention, the use of data mining is surrounded by a great deal of hype. Exaggerated reports tell of secrets that can be uncovered by setting algorithms loose on o...

Many problems of recent interest in statistics and machine learning can be posed in the framework of convex optimization. Due to the explosion in size and complexity of modern datasets, it is increasingly important to be...

BACKGROUND: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de fa...

Structural equation modeling (SEM) has become a quasi-standard in marketing and management research when it comes to analyzing the cause-effect relations between latent constructs. For most researchers, SEM is equivalent...

Outcomes of high-throughput biological experiments are typically interpreted by statistical testing for enriched gene functional categories defined by the Gene Ontology (GO). The resulting lists of GO terms may be large ...