NAGIOS: RODERIC FUNCIONANDO

Fast comparison of DNA sequences by oligonucleotide profiling

Repositori DSpace/Manakin

IMPORTANT: Aquest repositori està en una versió antiga des del 3/12/2023. La nova instal.lació está en https://roderic.uv.es/

Fast comparison of DNA sequences by oligonucleotide profiling

Mostra el registre parcial de l'element

dc.contributor.author Arnau Llombart, Vicente
dc.contributor.author Gallach Caballero, Miguel
dc.contributor.author Marín Lozano, Ignacio
dc.date.accessioned 2015-12-16T10:25:17Z
dc.date.available 2015-12-16T10:25:17Z
dc.date.issued 2008
dc.identifier.citation Arnau Llombart, Vicente Gallach Caballero, Miguel Marín Lozano, Ignacio 2008 Fast comparison of DNA sequences by oligonucleotide profiling BMC Research Notes 1 5 1 5
dc.identifier.uri http://hdl.handle.net/10550/49520
dc.description.abstract The comparison of DNA sequences is a traditional problem in genomics and bioinformatics. Many new opportunities emerge due to the improvement of personal computers, allowing the implementation of novel strategies of analysis. Findings: We describe a new program, called UVWORD, which determines the number of times that each DNA word present in a sequence (target) is found in a second sequence (source), a procedure that we have called oligonucleotide profiling. On a standard computer, the user may search for words of a size ranging from k = 1 to k = 14 nucleotides. Average counts for groups of contiguous words may also be established. The rate of analysis on standard computers is from 3.4 (k = 14) to 16 millions of words per second (1 ≤ k ≤ 8). This makes feasible the fast screening of even the longest known DNA molecules. Discussion: We show that the combination of the ability of analyzing words of relatively long size, which occur very rarely by chance, and the fast speed of the program allows to perform novel types of screenings, complementary to those provided by standard programs such as BLAST. This method can be used to determine oligonucleotide content, to characterize the distribution of repetitive sequences in chromosomes, to determine the evolutionary conservation of sequences in different species, to establish regions of similar DNA among chromosomes or genomes, etc.
dc.language.iso eng
dc.relation.ispartof BMC Research Notes, 2008, vol. 1, num. 5, p. 1-5
dc.subject Genòmica
dc.subject ADN
dc.title Fast comparison of DNA sequences by oligonucleotide profiling
dc.type journal article es_ES
dc.date.updated 2015-12-16T10:25:17Z
dc.identifier.doi 10.1186/1756-0500-1-5
dc.identifier.idgrec 052110
dc.rights.accessRights open access es_ES

Visualització       (234.6Kb)

Aquest element apareix en la col·lecció o col·leccions següent(s)

Mostra el registre parcial de l'element

Cerca a RODERIC

Cerca avançada

Visualitza

Estadístiques