Bioinformatics Glossary


A computerized storehouse of data that provides a standardized way for locating, adding, removing, and changing data. See also Object-oriented database, Relational database.

A form of a tree that lists the compared objects (e.g., sequences or genes in a microarray analysis) in a vertical order and joins related ones by levels of branches extending to one side of the list.

Depth (厚度)
See coverage

Dirichlet mixtures
Defined as the conjugational prior of a multinomial distribution. One use is for predicting the expected pattern of amino acid variation found in the match state of a hid-den Markov model (representing one column of a multiple sequence alignment of proteins), based on prior distributions found in conserved protein domains (blocks).

Distance in sequence analysis(序列距离)
The number of observed changes in an optimal alignment of two sequences, usually not counting gaps.

DNA Sequencing (DNA测序)
The experimental process of determining the nucleotide sequence of a region of DNA. This is done by labelling each nucleotide (A, C, G or T) with either a radioactive or fluorescent marker which identifies it. There are several methods of applying this technology, each with their advantages and disadvantages. For more information, refer to a current text book. High throughput laboratories frequently use automated sequencers, which are capable of rapidly reading large numbers of templates. Sometimes, the sequences may be generated more quickly than they can be characterised.

Domain (功能域)
A discrete portion of a protein assumed to fold independently of the rest of the protein and possessing its own function.

Dot matrix(点标矩阵图)
Dot matrix diagrams provide a graphical method for comparing two sequences. One sequence is written horizontally across the top of the graph and the other along the left-hand side. Dots are placed within the graph at the intersection of the same letter appearing in both sequences. A series of diagonal lines in the graph indicate regions of alignment. The matrix may be filtered to reveal the most-alike regions by scoring a minimal threshold number of matches within a sequence window.

Draft genome sequence (基因组序列草图)
The sequence produced by combining the information from the individual sequenced clones (by creating merged sequence contigs and then employing linking information to create scaffolds) and positioning the sequence along the physical map of the chromosomes.

DUST (一种低复杂性区段过滤程序)
A program for filtering low complexity regions from nucleic acid sequences.

Dynamic programming(动态规划法)
A dynamic programming algorithm solves a problem by combining solutions to sub-problems that are computed once and saved in a table or matrix. Dynamic programming is typically used when a problem has many possible solutions and an optimal one needs to be found. This algorithm is used for producing sequence alignments, given a scoring system for sequence comparisons.

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