String matching is seen as one of the essential problems in computer science. A variety of computer applications provide the string matching service for their end users. The remarkable boost in the number of data that is created and kept by modern computational devices influences researchers to obtain even more powerful methods for coping with this problem. In this research, the Quick Search st...

Sequencing by Hybridization (SBH) is a method for reconstructing an unknown DNA string based on substring queries: Using hybridization experiments, one can determine for each string in a given set of strings, whether the string appears in the target string, and use this information to reconstruct the target string. We study the problem when the queries are performed in rounds, where the queries...

Every DNA molecule can be described, avoiding its tridimensional structure, as a string (genome) of elements from a set of cardinality only four, whose elements (basis) can be listed as A, C, G, T. Sequences of DNA are repeated many times through the genome without yet understood biological function. DNA is in every living cells and whenever a cell duplicates itself every new offspring get a co...

A genetic sequence is simply a way of representing DNA, RNA, and proteins by a character string, an unbroken sequence of letters. A sequence has a finite length and contains only those characters belonging to a specified alphabet. An alphabet is a set of allowable characters. DNA uses a 4-character alphabet that consists of {A,C,G,T}. Likewise RNA uses a 4-character alphabet {A,C,G,U}. Proteins...

The preliminary research in the area of applications of neural networks and pattern matching algorithms in species classification is presented. Artificial neural networks for classification and different pattern matching algorithms for matching the given DNA patterns or strings with the existing DNA sequences available in the databases are specifically studied. A set of local searching algorith...

We examine the conformations of a model for short closed DNA. The molecule is represented as a cylindrically symmetric elastic string with a constraint corresponding to a specification of the linking number. We obtain analytic expressions for configuration, elastic energy, twist and linking number for a family of solutions spanning from a circle to a ’figure eight’. We suggest ways to use our c...

In this paper we consider using string matching in finding unique, gene specific oligonucleotides, which can be used for example in genomic research involving polymerase chain reaction, gene cloning, microarray technology or antisense DNA studies. Because of the typically huge size of genomes, the practical speed of the method used is important. We tested both exact and approximate string match...

The long-standing view of chromosome packaging is that 10-nm beads-on-a string chromatin fibres fold into higherorder 30-nm fibres, which further twist and coil to form highly condensed chromosomes. After four decades of intense pursuit of the structure and properties of 30-nm chromatin fibres, work of Nishino et al (2012) in this issue of The EMBO Journal demonstrates that regular 30-nm fibres...

Written text is considered as one of the oldest methods to represent knowledge. A text can be defined as a logical and consistent sequence of symbols which encodes information in a certain language. A straightforward example are natural languages, which are typically used by humans to communicate in spoken or written form. Other underlying examples are DNA, RNA and proteins sequences; DNA and R...

Described are two algorithms to find long approximate palindromes in a string, for example a DNA sequence. A simple algorithm requires O(n)space and almost always runs in O(k.n)-time where n is the length of the string and k is the number of “errors” allowed in the palindrome. Its worstcase time-complexity is O(n) but this does not occur with real biological sequences. A more complex algorithm ...