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BACKGROUND Ab initio protein structure prediction methods generate numerous structural candidates, which are referred to as decoys. The decoy with the most number of neighbors of up to a threshold distance is typically identified as the most representative decoy. However, the clustering of decoys needed for this criterion involves computations with runtimes(More)
The pattern languages are languages that are generated from patterns, and were first proposed by Angluin as a non-trivial class that is inferable from positive data [D. Angluin, Finding patterns common to a set of strings, Journal of Computer and System Sciences 21 (1980) 46–62; D. Angluin, Inductive inference of formal languages from positive data,(More)
BACKGROUND Co-expressing genes tend to cluster in eukaryotic genomes. This paper analyzes correlation between the proximity of eukaryotic genes and their transcriptional expression pattern in the zebrafish (Danio rerio) genome using available microarray data and gene annotation. RESULTS The analyses show that neighbouring genes are significantly(More)
Background: Horizontal gene transfer and gene duplication are two significant forces behind genome evolution. As more and more well-supported examples of HGTs are being revealed, there is a growing awareness that HGT is more widespread than previously thought, occurring often not only within bacteria, but also between species remotely related such as(More)
In this paper we examine the issues involved in finding consensus patterns from biosequence data of very small sample sizes, by searching for so-called minimal multiple generalization (mmg), that is, a set of syntactically minimal patterns that accounts for all the samples. The data we use are the sigma regulons with more conserved consensus patterns for(More)
In this paper we consider a basic clustering problem that has uses in bioinformat-ics. A structural fragment is a sequence of points in a 3D space, where is a fixed natural number. Two structural fragments f 1 and f 2 are equivalent if and only if f 1 = f 2 · R + τ under some rotation R and translation τ. We consider the distance between two structural(More)