A multilevel ant colony optimization algorithm for classical and isothermic DNA sequencing by hybridization with multiplicity information available

Computational Biology and Chemistry
Kamil KwarciakPiotr Formanowicz

Abstract

The classical sequencing by hybridization takes into account a binary information about sequence composition. A given element from an oligonucleotide library is or is not a part of the target sequence. However, the DNA chip technology has been developed and it enables to receive a partial information about multiplicity of each oligonucleotide the analyzed sequence consist of. Currently, it is not possible to assess the exact data of such type but even partial information should be very useful. Two realistic multiplicity information models are taken into consideration in this paper. The first one, called "one and many" assumes that it is possible to obtain information if a given oligonucleotide occurs in a reconstructed sequence once or more than once. According to the second model, called "one, two and many", one is able to receive from biochemical experiment information if a given oligonucleotide is present in an analyzed sequence once, twice or at least three times. An ant colony optimization algorithm has been implemented to verify the above models and to compare with existing algorithms for sequencing by hybridization which utilize the additional information. The proposed algorithm solves the problem with any kind of hybrid...Continue Reading

References

Oct 9, 1989·FEBS Letters·K R KhrapkoA D Mirzabekov
Jan 7, 2003·Nature Medicine·Robin L StearsMark Schena
Feb 12, 2004·Computational Biology and Chemistry·Jacek BłazewiczAleksandra Swiercz
Sep 2, 2006·Computational Biology and Chemistry·Jacek BlazewiczAleksandra Swiercz

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