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

Guillaume Blin, Guillaume Fertin, Danny Hermelin, Stéphane Vialette

Research output: Contribution to journalArticlepeer-review

8 Scopus citations


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.

Original languageEnglish
Pages (from-to)618-626
Number of pages9
JournalJournal of Discrete Algorithms
Issue number4
StatePublished - 1 Jan 2008
Externally publishedYes


  • Fixed-parameter tractability
  • Parameterized complexity
  • Protein similarity
  • Selenocysteine insertion
  • mRNA optimization

ASJC Scopus subject areas

  • Theoretical Computer Science
  • Discrete Mathematics and Combinatorics
  • Computational Theory and Mathematics


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