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.
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.
Lossy compressionIn information technology, lossy compression or irreversible compression is the class of data compression methods that uses inexact approximations and partial data discarding to represent the content. These techniques are used to reduce data size for storing, handling, and transmitting content. The different versions of the photo of the cat on this page show how higher degrees of approximation create coarser images as more details are removed. This is opposed to lossless data compression (reversible data compression) which does not degrade the data.
Rate–distortion theoryRate–distortion theory is a major branch of information theory which provides the theoretical foundations for lossy data compression; it addresses the problem of determining the minimal number of bits per symbol, as measured by the rate R, that should be communicated over a channel, so that the source (input signal) can be approximately reconstructed at the receiver (output signal) without exceeding an expected distortion D. Rate–distortion theory gives an analytical expression for how much compression can be achieved using lossy compression methods.
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.
Compression artifactA compression artifact (or artefact) is a noticeable distortion of media (including , audio, and video) caused by the application of lossy compression. Lossy data compression involves discarding some of the media's data so that it becomes small enough to be stored within the desired or transmitted (streamed) within the available bandwidth (known as the data rate or bit rate). If the compressor cannot store enough data in the compressed version, the result is a loss of quality, or introduction of artifacts.
Whole genome sequencingWhole genome sequencing (WGS), also known as full genome sequencing, complete genome sequencing, or entire genome sequencing, is the process of determining the entirety, or nearly the entirety, of the DNA sequence of an organism's genome at a single time. This entails sequencing all of an organism's chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast. Whole genome sequencing has largely been used as a research tool, but was being introduced to clinics in 2014.
Data compressionIn information theory, data compression, source coding, or bit-rate reduction is the process of encoding information using fewer bits than the original representation. Any particular compression is either lossy or lossless. Lossless compression reduces bits by identifying and eliminating statistical redundancy. No information is lost in lossless compression. Lossy compression reduces bits by removing unnecessary or less important information.
Dynamic range compressionDynamic range compression (DRC) or simply compression is an audio signal processing operation that reduces the volume of loud sounds or amplifies quiet sounds, thus reducing or compressing an audio signal's dynamic range. Compression is commonly used in sound recording and reproduction, broadcasting, live sound reinforcement and in some instrument amplifiers. A dedicated electronic hardware unit or audio software that applies compression is called a compressor.
DistortionIn signal processing, distortion is the alteration of the original shape (or other characteristic) of a signal. In communications and electronics it means the alteration of the waveform of an information-bearing signal, such as an audio signal representing sound or a video signal representing images, in an electronic device or communication channel. Distortion is usually unwanted, and so engineers strive to eliminate or minimize it. In some situations, however, distortion may be desirable.
Dynamic rangeDynamic range (abbreviated DR, DNR, or DYR) is the ratio between the largest and smallest values that a certain quantity can assume. It is often used in the context of signals, like sound and light. It is measured either as a ratio or as a base-10 (decibel) or base-2 (doublings, bits or stops) logarithmic value of the difference between the smallest and largest signal values. Electronically reproduced audio and video is often processed to fit the original material with a wide dynamic range into a narrower recorded dynamic range that can more easily be stored and reproduced; this processing is called dynamic range compression.
Vector quantizationVector quantization (VQ) is a classical quantization technique from signal processing that allows the modeling of probability density functions by the distribution of prototype vectors. It was originally used for data compression. It works by dividing a large set of points (vectors) into groups having approximately the same number of points closest to them. Each group is represented by its centroid point, as in k-means and some other clustering algorithms.
Clipping (signal processing)Clipping is a form of distortion that limits a signal once it exceeds a threshold. Clipping may occur when a signal is recorded by a sensor that has constraints on the range of data it can measure, it can occur when a signal is digitized, or it can occur any other time an analog or digital signal is transformed, particularly in the presence of gain or overshoot and undershoot. Clipping may be described as hard, in cases where the signal is strictly limited at the threshold, producing a flat cutoff; or it may be described as soft, in cases where the clipped signal continues to follow the original at a reduced gain.
Quantization (signal processing)Quantization, in mathematics and digital signal processing, is the process of mapping input values from a large set (often a continuous set) to output values in a (countable) smaller set, often with a finite number of elements. Rounding and truncation are typical examples of quantization processes. Quantization is involved to some degree in nearly all digital signal processing, as the process of representing a signal in digital form ordinarily involves rounding. Quantization also forms the core of essentially all lossy compression algorithms.
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.
CodecA codec is a device or computer program that encodes or decodes a data stream or signal. Codec is a portmanteau of coder/decoder. In electronic communications, an endec is a device that acts as both an encoder and a decoder on a signal or data stream, and hence is a type of codec. Endec is a portmanteau of encoder/decoder. A coder or encoder encodes a data stream or a signal for transmission or storage, possibly in encrypted form, and the decoder function reverses the encoding for playback or editing.
GenomeIn the fields of molecular biology and genetics, a genome is all the genetic information of an organism. It consists of nucleotide sequences of DNA (or RNA in RNA viruses). The nuclear genome includes protein-coding genes and non-coding genes, other functional regions of the genome such as regulatory sequences (see non-coding DNA), and often a substantial fraction of junk DNA with no evident function. Almost all eukaryotes have mitochondria and a small mitochondrial genome.
Shotgun sequencingIn genetics, shotgun sequencing is a method used for sequencing random DNA strands. It is named by analogy with the rapidly expanding, quasi-random shot grouping of a shotgun. The chain-termination method of DNA sequencing ("Sanger sequencing") can only be used for short DNA strands of 100 to 1000 base pairs. Due to this size limit, longer sequences are subdivided into smaller fragments that can be sequenced separately, and these sequences are assembled to give the overall sequence.
Pre-echoIn audio signal processing, pre-echo, sometimes called a forward echo, (not to be confused with reverse echo) is a digital audio compression artifact where a sound is heard before it occurs (hence the name). It is most noticeable in impulsive sounds from percussion instruments such as castanets or cymbals. It occurs in transform-based audio compression algorithms – typically based on the modified discrete cosine transform (MDCT) – such as MP3, MPEG-4 AAC, and Vorbis, and is due to quantization noise being spread over the entire transform-window of the codec.
Human genomeThe human genome is a complete set of nucleic acid sequences for humans, encoded as DNA within the 23 chromosome pairs in cell nuclei and in a small DNA molecule found within individual mitochondria. These are usually treated separately as the nuclear genome and the mitochondrial genome. Human genomes include both protein-coding DNA sequences and various types of DNA that does not encode proteins. The latter is a diverse category that includes DNA coding for non-translated RNA, such as that for ribosomal RNA, transfer RNA, ribozymes, small nuclear RNAs, and several types of regulatory RNAs.
