Teiresias algorithm

The Teiresias algorithm is a combinatorial algorithm for the discovery of rigid patterns (motifs) in biological sequences. It is named after the Greek prophet Teiresias and was created in 1997 by Isidore Rigoutsos and Aris Floratos.

The problem of finding sequence similarities in the primary structure of related proteins or genes is one of the problems arising in the analysis of biological sequences. It can be shown that pattern discovery in its general form is NP-hard. The Teiresias algorithm, is based on the observation that if a pattern spans many positions and appears exactly k times in the input then all fragments (sub patterns) of the pattern have to appear at least k times in the input. The algorithm is able to produce all patterns that have a user-defined number of copies in the given input, and manages to be very efficient by avoiding the enumeration of the entire space. Finally, the algorithm reports motifs that are maximal in both length and composition.

A new implementation of the Teiresias algorithm was recently made available by the Computational Medicine Center at Thomas Jefferson University. Teiresias is also accessible through an interactive web-based user interface by the same center. See external links for both.

Algorithm

In mathematics and computer science, an algorithm (ⁱ/ˈælɡərɪðəm/ AL-gə-ri-dhəm) is a self-contained step-by-step set of operations to be performed. Algorithms exist that perform calculation, data processing, and automated reasoning.

The words 'algorithm' and 'algorism' come from the name al-Khwārizmī. Al-Khwārizmī (Persian: خوارزمي‎‎, c. 780-850) was a Persian mathematician, astronomer, geographer, and scholar.

An algorithm is an effective method that can be expressed within a finite amount of space and time and in a well-defined formal language for calculating a function. Starting from an initial state and initial input (perhaps empty), the instructions describe a computation that, when executed, proceeds through a finite number of well-defined successive states, eventually producing "output" and terminating at a final ending state. The transition from one state to the next is not necessarily deterministic; some algorithms, known as randomized algorithms, incorporate random input.

Algorithm (disambiguation)

An algorithm is a self-contained step-by-step set of operations to be performed.

Algorithm may also refer to:

See also

Medical algorithm

A medical algorithm is any computation, formula, statistical survey, nomogram, or look-up table, useful in healthcare. Medical algorithms include decision tree approaches to healthcare treatment (e.g., if symptoms A, B, and C are evident, then use treatment X) and also less clear-cut tools aimed at reducing or defining uncertainty.

Scope

Medical algorithms are part of a broader field which is usually fit under the aims of medical informatics and medical decision making. Medical decisions occur in several areas of medical activity including medical test selection, diagnosis, therapy and prognosis, and automatic control of medical equipment.

In relation to logic-based and artificial neural network-based clinical decision support system, which are also computer applications to the medical decision making field, algorithms are less complex in architecture, data structure and user interface. Medical algorithms are not necessarily implemented using digital computers. In fact, many of them can be represented on paper, in the form of diagrams, nomographs, etc.