Valeria De Fonzo | PubMed Health

PubMed2003

STRING: finding tandem repeats in DNA sequences.

MOTIVATION AND RESULTS: The importance of Tandem Repeats in some genomes is now well established. We have reported elsewhere some interesting new results obtained by means of a preliminary program for finding Tandem Repeats in DNA sequences, together with a brief description of the basic ideas of the algorithm. We describe here a completely new program based only in part on those ideas, we briefly discuss the interpretation of the results, and, by way of example, we provide a few novel results relative to the parasites responsible of two re-emerging diseases, Plasmodium falciparum and Mycobacterium tuberculosis. Our program is portable, effective, powerful and fast: it can run on current desktop computers, and it finds all significant Tandem Repeats also in the longest segments of sequences in databases (up to millions of bases), in short times (minutes). AVAILABILITY: An academic version of the algorithm (full source listing in standard C language) can be freely downloaded (http://www.caspur.it/~castri/STRING/). SUPPLEMENTARY INFORMATION: Some illustrative figures and some sample results are provided as supplementary material at: http://www.caspur.it/~castri/STRING/

Algorithms↗

PubMedDate not supplied

A survey of dynamical genetics.

The classical view of genetics is based on the central dogma of molecular biology that assigns to DNA a fundamental but static role. According to the dogma, DNA can be duplicated only in identical copies (except for random errors), and no smart mechanism can alter the information content of DNA: in more detail, the direction of transfer of the genetic information is only from DNA through RNA to proteins and never backwards. However, starting from the so-called dynamic genome (McClintock's jumping genes), and the so-called dynamic mutations (such as the trinucleotide expansion or, more generally, the instability of the number of tandem repeats of longer sequences), there is now a growing body of important cases where it is known that the DNA is altered in a more or less sophisticated way, often by smart enzymatic mechanisms. The study of all such dynamic phenomena and of their interpretations can be naturally called dynamical genetics. In this survey we examine a number of such dynamic phenomena, and also some phenomena of great biological importance that have no universally accepted explanation within a static approach to genetics, and for which a dynamical interpretation has been only proposed. Important examples are some controversial but interesting phenomena such as horizontal transmission and Creutzfeldt-Jakob Disease, and those peculiar DNA structures known as G-quadruplexes.

Creutzfeldt-Jakob Syndrome↗