Fixed-parameter algorithms for protein similarity search under mRNA structure constraints

In the context of protein engineering, we consider the problem of computing an mRNA sequence of maximal codon-wise similarity to a given mRNA (and consequently, to a given protein) that additionally satisfies some secondary structure constraints, the so-called mRNA Structure Optimization ( MRSO) pro...

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Published in:	Journal of discrete algorithms (Amsterdam, Netherlands) Vol. 6; no. 4; pp. 618 - 626
Main Authors:	Blin, Guillaume, Fertin, Guillaume, Hermelin, Danny, Vialette, Stéphane
Format:	Journal Article
Language:	English
Published:	Elsevier B.V 2008 Elsevier
Subjects:	Bioinformatics Computational Complexity Computer Science Data Structures and Algorithms Fixed-parameter tractability Life Sciences mRNA optimization Parameterized complexity Protein similarity Quantitative Methods Selenocysteine insertion Selenocysteine insertion mRNA optimization Protein similarity Fixed-parameter tractability Parameterized complexity parameterized complexity protein similarity fixed-parameter tractability
ISSN:	1570-8667, 1570-8675
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Abstract	In the context of protein engineering, we consider the problem of computing an mRNA sequence of maximal codon-wise similarity to a given mRNA (and consequently, to a given protein) that additionally satisfies some secondary structure constraints, the so-called mRNA Structure Optimization ( MRSO) problem. Since MRSO is known to be APX -hard, Bongartz [D. Bongartz, Some notes on the complexity of protein similarity search under mRNA structure constraints, in: Proc. of the 30th Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM), 2004, pp. 174–183] suggested to attack the problem using the approach of parameterized complexity. In this paper we propose three fixed-parameter algorithms that apply for several interesting parameters of MRSO. We believe these algorithms to be relevant for practical applications today, as well as for possible future applications. Furthermore, our results extend the known tractability borderline of MRSO, and provide new research horizons for further improvements of this sort.
AbstractList	In the context of protein engineering, we consider the problem of computing an mRNA sequence of maximal codon-wise similarity to a given mRNA (and consequently, to a given protein) that additionally satisfies some secondary structure constraints, the so-called mRNA Structure Optimization ( MRSO) problem. Since MRSO is known to be APX -hard, Bongartz [D. Bongartz, Some notes on the complexity of protein similarity search under mRNA structure constraints, in: Proc. of the 30th Conference on Current Trends in Theory and Practice of Computer Science (SOFSEM), 2004, pp. 174–183] suggested to attack the problem using the approach of parameterized complexity. In this paper we propose three fixed-parameter algorithms that apply for several interesting parameters of MRSO. We believe these algorithms to be relevant for practical applications today, as well as for possible future applications. Furthermore, our results extend the known tractability borderline of MRSO, and provide new research horizons for further improvements of this sort. In the context of protein engineering, we consider the problem of computing an mRNA sequence of maximal codon-wise similarity to a given mRNA (and consequently, to a given protein) that additionally satisfies some secondary structure constraints, the so-called mRNA Structure Optimization (MRSO) problem. Since MRSO is known to be APX-hard, Bongartz [10] suggested to attack the problem using the approach of parameterized complexity. In this paper we propose three fixed-parameter algorithms that apply for several interesting parameters of MRSO. We believe these algorithms to be relevant for practical applications today, as well as for possible future applications. Furthermore, our results extend the known tractability borderline of MRSO, and provide new research horizons for further improvements of this sort.
Author	Vialette, Stéphane Hermelin, Danny Blin, Guillaume Fertin, Guillaume
Author_xml	– sequence: 1 givenname: Guillaume surname: Blin fullname: Blin, Guillaume email: gblin@univ-mlv.fr organization: IGM-LabInfo, UMR CNRS 8049, Université de Marne-la-Vallée, France – sequence: 2 givenname: Guillaume surname: Fertin fullname: Fertin, Guillaume email: guillaume.fertin@univ-nantes.fr organization: Laboratoire d'Informatique de Nantes-Atlantique (LINA), UMR CNRS 6241 Université de Nantes, 2 rue de la Houssinière, 44322 Nantes Cedex 3, France – sequence: 3 givenname: Danny surname: Hermelin fullname: Hermelin, Danny email: danny@cri.haifa.ac.il organization: Department of Computer Science, University of Haifa, Mount Carmel, Haifa, Israel – sequence: 4 givenname: Stéphane surname: Vialette fullname: Vialette, Stéphane email: vialette@univ-mlv.fr organization: IGM-LabInfo, UMR CNRS 8049, Université de Marne-la-Vallée, France
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Keywords	Selenocysteine insertion mRNA optimization Protein similarity Fixed-parameter tractability Parameterized complexity parameterized complexity protein similarity fixed-parameter tractability
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SubjectTerms	Bioinformatics Computational Complexity Computer Science Data Structures and Algorithms Fixed-parameter tractability Life Sciences mRNA optimization Parameterized complexity Protein similarity Quantitative Methods Selenocysteine insertion
Title	Fixed-parameter algorithms for protein similarity search under mRNA structure constraints
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