Evolutionary Construction of Multiple Graph Alignments for Mining Structured Biomolecular Data
نویسندگان
چکیده
The concept of multiple graph alignment has recently been introduced as a novel method for the structural analysis of biomolecules. Using inexact, approximate graph-matching techniques, this method enables the robust identification of approximately conserved patterns in biologically related structures. In particular, using multiple graph alignments, it is possible to characterize functional protein families independent of sequence or fold homology. This paper first recalls the concept of multiple graph alignment and then addresses the problem of computing optimal alignments from an algorithmic point of view. In this regard, a method from the field of evolutionary algorithms is proposed and empirically compared to a hitherto existing greedy strategy.
منابع مشابه
Supplementary Material to Evolutionary Construction of Multiple Graph Alignments for the Structural Analysis of Biomolecules
متن کامل
Evolutionary Construction of Multiple Graph Alignments for the Structural Analysis of Biomolecules
The concept of multiple graph alignment (MGA) has recently been introduced as a novel method for the structural analysis of biomolecules. Using approximate graph matching techniques, this method enables the robust identification of approximately conserved patterns in biologically related structures. In particular, MGA enables the characterization of functional protein families independent of se...
متن کاملAn Evolutionary Algorithm for the Maximum Weight Trace Formulation of the Multiple Sequence Alignment Problem
The multiple sequence alignment problem (MSA) can be reformulated as the problem of finding a maximum weight trace in an alignment graph, which is derived from all pairwise alignments. We improve the alignment graph by adding more global information. A new construction heuristic and an evolutionary algorithm with specialized operators are proposed and compared to three other algorithms for the ...
متن کاملDetermination of constant coefficients of Bourgoyne and Young drilling rate model using a novel evolutionary algorithm
Achieving minimum cost and time in reservoir drilling requires evaluating the effects of the drilling parameters on the penetration rate and constructing a drilling rate estimator model. Several drilling rate models have been presented using the drilling parameters. Among these, the Bourgoyne and Young (BY) model is widely utilized in order to estimate the penetration rate. This model relates s...
متن کاملThe global trace graph, a novel paradigm for searching protein sequence databases
MOTIVATION Propagating functional annotations to sequence-similar, presumably homologous proteins lies at the heart of the bioinformatics industry. Correct propagation is crucially dependent on the accurate identification of subtle sequence motifs that are conserved in evolution. The evolutionary signal can be difficult to detect because functional sites may consist of non-contiguous residues w...
متن کامل