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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)
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)
We consider the problem of finding a set of patterns that best characterizes a set of strings. To this end, Arimura et. al. [3] considered the use of minimal multiple generalizations (mmg) for such characterizations. Given any sample set, the mmgs are, roughly speaking, the most (syntactically) specific set of languages containing the sample within a given(More)
In inductive inference, a machine is given words of a language (a recursively enu-merable set in our setting) and the machine is said to identify the language if it correctly names the language. In this paper we study identifiability of classes of languages where the unions of up to a fixed number (n say) of languages from the class are provided as input.(More)