数据库

Multiple Sequence Alignment (MSA) is an essential tool in protein structure modeling, gene and protein function prediction, DNA motif recognition, phylogenetic analysis, and many other bioinformatics tasks. Therefore, improving the accuracy of multiple sequence alignment is ...

Multiple sequence alignment (MSA) is an essential tool with many applications in bioinformatics and computational biology. Accurate MSA construction for divergent proteins remains a difficult computational task. The constantly increasing protein sequences and structu ...

Profile ALIgNmEnt (PRALINE) is a versatile multiple sequence alignment toolkit. In its main alignment protocol, PRALINE follows the global progressive alignment algorithm. It provides various alignment optimization strategies to address the different situations that call ...

SAT� is a method for estimating multiple sequence alignments and trees that has been shown to produce highly accurate results for datasets with large numbers of sequences. Running SAT� using its default settings is very simple, but improved accuracy can be obtained by modifying its algorithm ...

Multiple sequence alignment (MSA) generally constitutes the foundation of many bioinformatics studies involving functional, structural, and evolutionary relationship analysis between sequences. As a result of the exponential computational complexity of the exact app ...

PicXAA is a probabilistic nonprogressive alignment algorithm that finds protein (or DNA) multiple sequence alignments with maximum expected accuracy. PicXAA greedily builds up the alignment from sequence regions with high local similarity, thereby yielding an accurate glob ...

DIALIGN is a software tool for multiple sequence alignment by combining global and local alignment features. It composes multiple alignments from local pairwise sequence similarities. This approach is particularly useful to discover conserved functional regions in sequences ...

Multiple sequence alignment involves identifying related subsequences among biological sequences. When matches are found, the associated pieces are shifted so that when sequences are presented as successive rows—one sequence per row—homologous residues line-up in columns. ...

Evolutionary analyses require sequence alignments that correctly represent evolutionary homology. Evolutionary and structural homology are not the same and sequence alignments generated with methods designed for structural matching can be seriously misleading in com ...

BLAST, FASTA, and other similarity searching programs seek to identify homologous proteins and DNA sequences based on excess sequence similarity. If two sequences share much more similarity than expected by chance, the simplest explanation for the excess similarity is common ancest ...

Multiple sequence alignment (MSA) is a fundamental and ubiquitous technique in bioinformatics used to infer related residues among biological sequences. Thus alignment accuracy is crucial to a vast range of analyses, often in ways difficult to assess in those analyses. To compare the per ...

Multiple sequence alignment involves alignment of more than two sequences and is an NP-complete problem. Therefore, heuristic algorithms that use different criteria to find an approximation to the optimal solution are employed. At the heart of these approaches lie the scoring and objec ...

Computation of multiple sequence alignment (MSA) is usually formulated as a combinatory optimization problem of an objective function. Solving the problem for virtually all sensible objective functions is known to be NP-complete implying that some heuristics must be adopted. Seve ...

Independent scoring of the aligned sections to determine the quality of biological sequence alignments enables recursive definitions of the overall alignment score. This property is not only biologically meaningful but it also provides the opportunity to find the optimal alignm ...

BioModels Database is a public online resource that allows storing and sharing of published, peer-reviewed quantitative, dynamic models of biological processes. The model components and behaviour are thoroughly checked to correspond the original publication and manually cur ...

This chapter describes the Systems Biology Markup Language (SBML) from its origins. It describes the rationale behind and importance of having a common language when it comes to representing models. This chapter mentions the development of SBML and outlines the structure of an SBML model. It p ...

The aim of this chapter is to provide sufficient information to enable a reader, new to the subject of Systems Biology, to create and use effectively controlled annotations, using resolvable Identifiers.org Uniform Resource Identifiers (URIs). The text details the underlying require ...

A growing realization of the importance of stochasticity in cell and molecular processes has stimulated the need for statistical models that incorporate intrinsic (and extrinsic) variability. In this chapter we consider stochastic kinetic models of reaction networks leading to a M ...

Chemical kinetics is the study of the rate of reactions transforming some chemical entities into other chemical entities. Over the twentieth century it has become one of the cornerstones of biochemistry. When in the second half of the century basic knowledge of cellular processes became suf ...

The Biological Network Manager (BiNoM) is a software tool for the manipulation and analysis of biological networks. It facilitates the import and conversion of a set of well-established systems biology file formats. It also provides a large set of graph-based algorithms that allow users to a ...