TY - GEN
T1 - Fixed-parameter algorithms for protein similarity search under mRNA structure constraints
AU - Blin, Guillaume
AU - Fertin, Guillaume
AU - Hermelin, Danny
AU - Vialette, Stéphane
PY - 2005/1/1
Y1 - 2005/1/1
N2 - 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 MRSO problem [2], Since the MRSO problem is known to be APX-hard [8], Bongartz proposed in [8] to attack the problem using the concept of parameterized complexity. In this paper we follow this suggested approach by devising fixed-parameter algorithms for several interesting parameters of MRSO. We believe these algorithms to be relevant for practical applications today, as well as for several future applications. Furthermore, our results extend the known tractability borderline of MRSO, and provide new research horizons for further improvements of this sort.
AB - 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 MRSO problem [2], Since the MRSO problem is known to be APX-hard [8], Bongartz proposed in [8] to attack the problem using the concept of parameterized complexity. In this paper we follow this suggested approach by devising fixed-parameter algorithms for several interesting parameters of MRSO. We believe these algorithms to be relevant for practical applications today, as well as for several future applications. Furthermore, our results extend the known tractability borderline of MRSO, and provide new research horizons for further improvements of this sort.
UR - http://www.scopus.com/inward/record.url?scp=33744931676&partnerID=8YFLogxK
U2 - 10.1007/11604686_24
DO - 10.1007/11604686_24
M3 - Conference contribution
AN - SCOPUS:33744931676
SN - 3540310002
SN - 9783540310006
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 271
EP - 282
BT - Graph-Theoretic Concepts in Computer Science - 31st International Workshop, WG 2005, Revised Selected Papers
PB - Springer Verlag
T2 - 31st International Workshop on Graph-Theoretic Concepts in Computer Science, WG 2005
Y2 - 23 June 2005 through 25 June 2005
ER -