Bioinformatics Glossary


Radiation hybrid (RH) map (辐射杂交图谱)
A genome map in which STSs are positioned relative to one another on the basis of the frequency with which they are separated by radiation-induced breaks. The frequency is assayed by analysing a panel of human–hamster hybrid cell lines, each produced by lethally irradiating human cells and fusing them with recipient hamster cells such that each carries a collection of human chromosomal fragments. The unit of distance is centirays (cR), denoting a 1% chance of a break occuring between two loci

Raw Score (初值,指最初得到的联配值S)
The score of an alignment, S, calculated as the sum of substitution and gap scores. Substitution scores are given by a look-up table (see PAM, BLOSUM). Gap scores are typically calculated as the sum of G, the gap opening penaltyand L, the gap extension penalty. For a gap of length n, the gap cost would be G+Ln. The choice of gap costs, G and L is empirical, but it is customary to choose a high value for G (10-15)and a low value for L (1-2).

Raw sequence (原始序列/读胶序列)
Individual unassembled sequence reads, produced by sequencing of clones containing DNA inserts.

Receiver operator characteristic
The receiver operator characteristic (ROC) curve describes the probability that a test will correctly declare the condition present against the probability that the test will declare the condition present when actually absent. This is shown through a graph of the tesls sensitivity against one minus the test specificity for different possible threshold values.

Redundancy (冗余)
The presence of more than one identical item represents redundancy. In bioinformatics, the term is used with reference to the sequences in a sequence database. If a database is described as being redundant, more than one identical (redundant) sequence may be found. If the database is said to be non-redundant (nr), the database managers have attempted to reduce the redundancy. The term is ambiguous with reference to genetics, and as such, the degree of non-redundancy varies according to the database manager's interpretation of the term. One can argue whether or not two alleles of a locus defines the limit of redundancy, or whether the same locus in different, closely related organisms constitutes redundency. Non-redundant databases are, in some ways, superior, but are less complete. These factors should be taken into consideration when selecting a database to search.

Regular expressions
This computational tool provides a method for expressing the variations found in a set of related sequences including a range of choices at one position, insertions, repeats, and so on. For example, these expressions are used to characterize variations found in protein domains in the PROSITE catalog.

A set of techniques for reducing data overfitting when training a model. See also Overfitting.

Relational database(关系数据库)
Organizes information into tables where each column represents the fields of informa-tion that can be stored in a single record. Each row in the table corresponds to a single record. A single database can have many tables and a query language is used to access the data. See also Object-oriented database.

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