Information theoretical probe selection for hybridisation experiments | Zendy

Ralf Herwig | Zendy; Armin O. Schmitt | Zendy; Matthias Steinfath | Zendy; John O’Brien | Zendy; Henrik Seidel | Zendy; Sebastian MeierEwert | Zendy; Hans Lehrach | Zendy; Uwe Radelof | Zendy

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Information theoretical probe selection for hybridisation experiments

Author(s) -

Ralf Herwig,

Armin O. Schmitt,

Matthias Steinfath,

John O’Brien,

Henrik Seidel,

Sebastian MeierEwert,

Hans Lehrach,

Uwe Radelof

Publication year - 2000

Publication title -

bioinformatics

Language(s) - English

Resource type - Journals

SCImago Journal Rank - 3.599

H-Index - 390

eISSN - 1367-4811

pISSN - 1367-4803

DOI - 10.1093/bioinformatics/16.10.890

Subject(s) - executable , computer science , data mining , set (abstract data type) , oligomer restriction , pipeline (software) , file transfer protocol , selection (genetic algorithm) , algorithm , identification (biology) , pattern recognition (psychology) , artificial intelligence , oligonucleotide , biology , the internet , dna , genetics , programming language , botany , world wide web

The choice of probes is an important feature of hybridisation experiments. In this paper we present an algorithm that optimises probes with respect to a training set of sequences based on Shannon entropy as a quality criterion. The practical motivation for our algorithm is oligonucleotide fingerprinting, a method for the simultaneous identification of sequences (cDNA or genomic DNA) by their hybridisation tags according to a set of short probes such as octamers, although the algorithm is of course not restricted to that application.

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