A nonempty circular string C(x) of length n is said to be covered by a set U k of strings each of xed length k n ii every position in C(x) lies within an occurrence of some string u 2 U k. In this paper we consider the problem of determining the minimum cardinality of a set U k which guarantees that every circular string C(x) of length n k can be covered. In particular, we show how, for any pos...

Approximate string matching with k-differences has a number of practical applications, ranging from pattern recognition to computational biology. This paper proposes an efficient memory-access algorithm for parallel approximate string matching with k-differences on Graphics Processing Units (GPUs). In the proposed algorithm, all threads in the same GPUs warp share data using warp-shuffle operat...

AQL stands for Alignment Query Language, and it is an extension of SQL. AQL allows for declarative querying of databases containing strings of characters as entries. For instance, in applications such as genomic databases, the DNA-sequences are strings, and they need to be queried based on their structure. The LIKE-operation in SQL does not go very far. Existing systems for string databases hav...

In eucaryotic cells, DNA is bound to various proteins and forms a complex nucleoprotein structure called chromatin. Indispensable and ubiquitous chromatin components are histones, small proteins of highly conserved primary structure. Two molecules of each H2A, H2B, H3 and H4 type, form the nucleosomal core around which a 146 base pair (bp) stretch of DNA is wrapped. Histone H1 is bound to about...

We have applied chromatin sequencing technology to the euryarchaeon Thermococcus kodakarensis, which is known to possess histone-like proteins. We detect positioned chromatin particles of variable sizes associated with lengths of DNA differing as multiples of 30 bp (ranging from 30 bp to >450 bp) consistent with formation from dynamic polymers of the archaeal histone dimer. T. kodakarensis chro...

according to the temperature distribution of water injection well-bore in highly deviated wells under different conditions and unstable temperature field heat conduction principles, a true three-dimensional model was established to analyze the law of variation on temperature of highly deviated wells during the water injection process, and to analyze the factors that influence the water injectio...

Due to newly developed high-throughput technologies for DNA sequencing, the number of fully sequenced species increases rapidly. String databases holding these sequences are very large. On the eld of molecular biology the handling of large string data which cannot be broken in words is a great challenge. Hereby the most important string operation is the approximate substring match. This type of...