Bioinformatics glossary - L

Bioinformatics glossary - L

Linkage

The tendency of two or more genes on the same chromosome to be inherited together. The closer two genes are on a chromosome, the more likely it is that they will be inherited together.

Leucine zipper

A motif found in certain proteins in which Leu residues are evenly

spaced through an a-helical region, such that they would end up on the same face of the helix. Dimers can form between two such proteins. The Leu zipper is important in the function of transcription factors such as Fos and Jun and related proteins.

Leukaemia

Cancer that begins in developing blood cells in the bone marrow

Library

A library might be either a genomic library, or a cDNA library. In either case, the library is just a tube carrying a mixture of thousands of different clones - bacteria or l phages. Each clone carries an "insert" - the cloned DNA.

Ligand

Any small molecule that binds to a protein or receptor; the cognate partner of many cellular proteins, enzymes, and receptors. 

Log-odds

A score created by taking the logarithm of the observed probability of an replacement divided by the expected probability of the replacement. In general log-odds scores in sequence alignment reduce a multiplication problem (with probabilities) to an addition problem (using log-odds numbers). This approach is generally much less expensive computationally.

Lipid

A diverse class of compounds found in all living cells whose main biological functions include storing energy, cellular signalling, and acting as structural components of cellular membranes.

Lipoprotein

An assembly of both proteins and lipids that functions to transport water insoluble fats throughout the vascular and lymphatic systems.

Lipoprotein Lipase (LPL)

An enzyme that plays a critical role in transporting fats and breaking down fat carrying molecules called lipoproteins.

Ligase

An enzyme, T4 DNA ligase, which can link pieces of DNA together. The pieces must have compatible ends (both of them blunt, or else mutually compatible sticky ends), and the ligation reaction requires ATP.

Ligation

The process of splicing two pieces of DNA together. In practice, a pool of DNA fragments are treated with ligase (see "Ligase") in the presence of ATP, and all possible splicing products are produced, including circularised forms and end-to-end ligation of 2, 3 or more pieces. Usually, only some of these products are useful, and the investigator must have some way of selecting the desirable one.

Lindna

An EMBOSS application. The program 'lindna' draws linear maps of DNA constructs. It uses the graphical shapes: ticks, ranges, and blocks to represent genetic markers (e.g, genes and ESTs) and places them according to their position in a DNA fragment. The markers can be organised in different groups. The program reads in one input file in which the user specifies the names and positions of the genetic markers. In this file the user also enters data for controlling the appearance of the markers. A refined customisation of the drawing can be achieved by running the program with '-options' on the command line and changing the values of the desired parameters.

Linkage

The association of genes (or genetic loci) on the same chromosome. Genes that are linked together tend to be transmitted together.

Linkage map

A genetic map of a chromosome or genome delineated by mapping the

positions of genes to their chromosomes by their linkage to readily identifiable genetic loci.

Listor

An EMBOSS application. listor reads in two sets of sequences and writes out a list file (file of file names) that result from the logical union of these two sets of sequences. It is a simple way of manipulating and editing lists or sets of sequences to produce a list file. When comparing sequences to see if they are the same between two sets of sequences, no use is made of the ID name or accession number of the sequences. Only the sequences themselves are compared. The comparison of the sequences is case-independent. The logical union is an OR operation by default. Other available operations are: AND, XOR and NOT. The (default) logical OR of the two sets of sequences is simply the result of merging the two sets of sequences, (without listing any shared sequences twice). A logical AND simply lists those sequences that occur in both sets of sequences. A logical XOR lists those sequences that ONLY occur in the first set or only occur in the second set - sequences occuring in both sets are ignored (the opposite of an AND). A logical NOT lists all those sequences in the first set except for those that also occur in the second set.

Local alignment

An alignment that searches for segments of the two sequences that

match well. There is no attempt to force entire sequences into an alignment, just those parts that appear to have good similarity, according to some criterion.

Locus

The specific position occupied by a gene on a chromosome. At a given locus, any one of the variant forms of a gene may be present. The variants are said to be alleles of that gene. 

"Lab on a chip"

Term describing microdevices that allow rapid, microanalytical analysis of DNA or protein in a single, fully integrated system. Typically, these devices are miniature surfaces, made of silicon, glass or plastic, which carry the necessary microdevices (pumps, valves, microfluidic controllers, and detectors) that allow sample separation and analysis. These devices are used in drug discovery, genetic testing and separation science.

Lead compound

A candidate compound identified as the best "hit" (tight binder) after screening of a combinatorial (or other) compound library, that is then taken into further rounds of screening to determine its suitability as a drug.

Lead optimization

The process of converting a putative lead compound ("hit") into a therapeutic drug with maximal activity and minimal side affects, typically using a combination of computer-based drug design, medicinal chemistry and pharmacology.

Lexicon

In Bioinformatics, a lexicon refers to a pre-defined list of terms that together completely define the contents of a particular database. 

(strict.) The component in the grammar which is in bare form a list of words or lexical entries.

Linkage map

A genetic map of a chromosome or genome delineated by mapping the positions of genes to their chromosomes by their linkage to readily identifiable genetic loci.

Locus

The specific position occupied by a gene on a chromosome. At a given locus, any one of the variant forms of a gene may be present. The variants are said to be alleles of that gene.

LASTz
A sequence alignment program that can align two large DNA sequences (for example human chromosomes) and scores the alignment. Supported at the Miller Lab http://www.bx.psu.edu/~rsharris/lastz/

LC-MS
Liquid chromatography–mass spectrometry (LC-MS) is a powerful analytical technique that combines liquid chromatography (used to identify individual components in a mixture of compounds) and mass spectrometry (measures the mass-to-charge ratio of charged particles).

Leukotoxin
A protein toxin secreted from the oral bacterium

Likelihood
Likelihood is an approach of statistical inference, also known as frequentist statistics, where conclusions are made from sample data by the emphasis on the frequency or proportion of the data. The likelihood function is a statistical procedures that returns a value that is proportional to the probability of a model and parameters, given the data that is observed.

Lipid
Lipids are a broad group of hydrophobic small molecules. They function as the energy storage and are structural components of cell membranes. Lipids are also important signaling molecules (e.g. steroid hormones).

Lipinski's rule of five
A list of five properties a compound must have to increase its chances of being a potential drug candidate.

lncRNA
Long non-coding RNA molecules that are typically greater than 200bp in length and do not belong to any other class of non-coding RNA. See controlled vocabulary for ncRNA classes.

Local alignment
An alignment that searches for segments of the two sequences that match well. There is no attempt to force entire sequences into an alignment, just those parts that appear to have good similarity.

LogP
logP also known as the partition-coefficient (P) is the ratio of concentrations of a compound in a mixture of two immiscible phases at equilibrium. This is used to measure the difference in solubility of the compound in these two phases.

Lookup table
An array of data values that can be quickly accessed by a computer programme to convert data from one form to another.

Lucene
Lucene is a text search engine library written in Java. In a Lucene query, the query is broken up into terms and operators. There are two types of terms: Single Terms and Phrases. A Single Term is a single word such as "test" or "hello". A Phrase is a group of words surrounded by double quotes such as "hello dolly". Lucene supports fielded data (as the literature records are). When performing a search you can either specify a field, or use the default field.