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Minimizing sets of enzymes to differentiate between species
July 2010
BuAB10
A large number of species cannot be distinguished via standard non genetic analysis in the lab. In this paper we address the problem of finding minimum sets of restriction enzymes that can be used to unequivocally identify the species of a yeast specimen by analyzing the size of digested DNA fragments in gel electrophoresis experiments. The problem is first mapped into set covering and then solved using Constraint Programming techniques. Although the data sets used are relatively small (23 yeast species and 331 enzymes), a similar approach might be applicable to larger ones and to a number of variants as it is dis- cussed in the conclusion. The subject of this paper has already raised the interest of our biologist partners and may become a benchmark for the application of Constraint Programming techniques to Bioinformatics.
In proceedings
David Buezas, João Almeida, Pedro Barahona
Alessandro Dal Palu, Agostino Dovier, Sebastian Will
Proceedings of WCB 2010 -Proceedings of WCB 2010 Workshop on Constraint Based Methods for Bioinformatics
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http://wcb10.dimi.uniud.it/
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David Buezas and João Almeida and Pedro Barahona, Minimizing sets of enzymes to differentiate between species, in: Alessandro Dal Palu and Agostino Dovier and Sebastian Will (eds), Proceedings of WCB 2010 -Proceedings of WCB 2010 Workshop on Constraint Based Methods for Bioinformatics, http://wcb10.dimi.uniud.it/, July 2010.
David Buezas, João Almeida and <a href="/people/members/view.php?code=7e27bc13fad97e99cd21ea6914d55659" class="author">Pedro Barahona</a>, <b>Minimizing sets of enzymes to differentiate between species</b>, in: Alessandro Dal Palu, Agostino Dovier and Sebastian Will (eds), <u>Proceedings of WCB 2010 -Proceedings of WCB 2010 Workshop on Constraint Based Methods for Bioinformatics</u>, http://wcb10.dimi.uniud.it/, July 2010.
@inproceedings {BuAB10, author = {David Buezas and Jo{\~a}o Almeida and Pedro Barahona}, editor = {Alessandro Dal Palu and Agostino Dovier and Sebastian Will}, title = {Minimizing sets of enzymes to differentiate between species}, booktitle = {Proceedings of WCB 2010 -Proceedings of WCB 2010 Workshop on Constraint Based Methods for Bioinformatics}, address = {http://wcb10.dimi.uniud.it/}, abstract = {A large number of species cannot be distinguished via standard non genetic analysis in the lab. In this paper we address the problem of finding minimum sets of restriction enzymes that can be used to unequivocally identify the species of a yeast specimen by analyzing the size of digested DNA fragments in gel electrophoresis experiments. The problem is first mapped into set covering and then solved using Constraint Programming techniques. Although the data sets used are relatively small (23 yeast species and 331 enzymes), a similar approach might be applicable to larger ones and to a number of variants as it is dis- cussed in the conclusion. The subject of this paper has already raised the interest of our biologist partners and may become a benchmark for the application of Constraint Programming techniques to Bioinformatics.}, month = {July}, year = {2010}, }
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