Sequence alignmentIn bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences. Aligned sequences of nucleotide or amino acid residues are typically represented as rows within a matrix. Gaps are inserted between the residues so that identical or similar characters are aligned in successive columns.
Multiple sequence alignmentMultiple sequence alignment (MSA) may refer to the process or the result of sequence alignment of three or more biological sequences, generally protein, DNA, or RNA. In many cases, the input set of query sequences are assumed to have an evolutionary relationship by which they share a linkage and are descended from a common ancestor. From the resulting MSA, sequence homology can be inferred and phylogenetic analysis can be conducted to assess the sequences' shared evolutionary origins.
Time complexityIn computer science, the time complexity is the computational complexity that describes the amount of computer time it takes to run an algorithm. Time complexity is commonly estimated by counting the number of elementary operations performed by the algorithm, supposing that each elementary operation takes a fixed amount of time to perform. Thus, the amount of time taken and the number of elementary operations performed by the algorithm are taken to be related by a constant factor.
Computational complexityIn computer science, the computational complexity or simply complexity of an algorithm is the amount of resources required to run it. Particular focus is given to computation time (generally measured by the number of needed elementary operations) and memory storage requirements. The complexity of a problem is the complexity of the best algorithms that allow solving the problem. The study of the complexity of explicitly given algorithms is called analysis of algorithms, while the study of the complexity of problems is called computational complexity theory.
Randomized algorithmA randomized algorithm is an algorithm that employs a degree of randomness as part of its logic or procedure. The algorithm typically uses uniformly random bits as an auxiliary input to guide its behavior, in the hope of achieving good performance in the "average case" over all possible choices of random determined by the random bits; thus either the running time, or the output (or both) are random variables.
Parameterized complexityIn computer science, parameterized complexity is a branch of computational complexity theory that focuses on classifying computational problems according to their inherent difficulty with respect to multiple parameters of the input or output. The complexity of a problem is then measured as a function of those parameters. This allows the classification of NP-hard problems on a finer scale than in the classical setting, where the complexity of a problem is only measured as a function of the number of bits in the input.
Computational complexity theoryIn theoretical computer science and mathematics, computational complexity theory focuses on classifying computational problems according to their resource usage, and relating these classes to each other. A computational problem is a task solved by a computer. A computation problem is solvable by mechanical application of mathematical steps, such as an algorithm. A problem is regarded as inherently difficult if its solution requires significant resources, whatever the algorithm used.
Complexity classIn computational complexity theory, a complexity class is a set of computational problems "of related resource-based complexity". The two most commonly analyzed resources are time and memory. In general, a complexity class is defined in terms of a type of computational problem, a model of computation, and a bounded resource like time or memory. In particular, most complexity classes consist of decision problems that are solvable with a Turing machine, and are differentiated by their time or space (memory) requirements.
Sequence analysisIn bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand its features, function, structure, or evolution. Methodologies used include sequence alignment, searches against biological databases, and others. Since the development of methods of high-throughput production of gene and protein sequences, the rate of addition of new sequences to the databases increased very rapidly.
Space complexityThe space complexity of an algorithm or a computer program is the amount of memory space required to solve an instance of the computational problem as a function of characteristics of the input. It is the memory required by an algorithm until it executes completely. This includes the memory space used by its inputs, called input space, and any other (auxiliary) memory it uses during execution, which is called auxiliary space. Similar to time complexity, space complexity is often expressed asymptotically in big O notation, such as etc.
Reduction (complexity)In computability theory and computational complexity theory, a reduction is an algorithm for transforming one problem into another problem. A sufficiently efficient reduction from one problem to another may be used to show that the second problem is at least as difficult as the first. Intuitively, problem A is reducible to problem B, if an algorithm for solving problem B efficiently (if it existed) could also be used as a subroutine to solve problem A efficiently. When this is true, solving A cannot be harder than solving B.
Program optimizationIn computer science, program optimization, code optimization, or software optimization, is the process of modifying a software system to make some aspect of it work more efficiently or use fewer resources. In general, a computer program may be optimized so that it executes more rapidly, or to make it capable of operating with less memory storage or other resources, or draw less power. Although the word "optimization" shares the same root as "optimal", it is rare for the process of optimization to produce a truly optimal system.
Optimizing compilerIn computing, an optimizing compiler is a compiler that tries to minimize or maximize some attributes of an executable computer program. Common requirements are to minimize a program's execution time, memory footprint, storage size, and power consumption (the last three being popular for portable computers). Compiler optimization is generally implemented using a sequence of optimizing transformations, algorithms which take a program and transform it to produce a semantically equivalent output program that uses fewer resources or executes faster.
Substitution matrixIn bioinformatics and evolutionary biology, a substitution matrix describes the frequency at which a character in a nucleotide sequence or a protein sequence changes to other character states over evolutionary time. The information is often in the form of log odds of finding two specific character states aligned and depends on the assumed number of evolutionary changes or sequence dissimilarity between compared sequences. It is an application of a stochastic matrix.
Conserved sequenceIn evolutionary biology, conserved sequences are identical or similar sequences in nucleic acids (DNA and RNA) or proteins across species (orthologous sequences), or within a genome (paralogous sequences), or between donor and receptor taxa (xenologous sequences). Conservation indicates that a sequence has been maintained by natural selection. A highly conserved sequence is one that has remained relatively unchanged far back up the phylogenetic tree, and hence far back in geological time.
Structural alignmentStructural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules. In contrast to simple structural superposition, where at least some equivalent residues of the two structures are known, structural alignment requires no a priori knowledge of equivalent positions.
Protein sequencingProtein sequencing is the practical process of determining the amino acid sequence of all or part of a protein or peptide. This may serve to identify the protein or characterize its post-translational modifications. Typically, partial sequencing of a protein provides sufficient information (one or more sequence tags) to identify it with reference to databases of protein sequences derived from the conceptual translation of genes. The two major direct methods of protein sequencing are mass spectrometry and Edman degradation using a protein sequenator (sequencer).
Mathematical optimizationMathematical optimization (alternatively spelled optimisation) or mathematical programming is the selection of a best element, with regard to some criterion, from some set of available alternatives. It is generally divided into two subfields: discrete optimization and continuous optimization. Optimization problems arise in all quantitative disciplines from computer science and engineering to operations research and economics, and the development of solution methods has been of interest in mathematics for centuries.
Peephole optimizationPeephole optimization is an optimization technique performed on a small set of compiler-generated instructions; the small set is known as the peephole or window. Peephole optimization involves changing the small set of instructions to an equivalent set that has better performance.
Nucleic acid sequenceA nucleic acid sequence is a succession of bases within the nucleotides forming alleles within a DNA (using GACT) or RNA (GACU) molecule. This succession is denoted by a series of a set of five different letters that indicate the order of the nucleotides. By convention, sequences are usually presented from the 5' end to the 3' end. For DNA, with its double helix, there are two possible directions for the notated sequence; of these two, the sense strand is used.
