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Open Access Open Badges Technical Note

Fast comparison of DNA sequences by oligonucleotide profiling

Vicente Arnau1, Miguel Gallach2 and Ignacio Marín3*

Author Affiliations

1 Departamento de Informática. Universidad de Valencia, Spain

2 Departamento de Genética. Universidad de Valencia, Spain

3 Instituto de Biomedicina de Valencia. Consejo Superior de Investigaciones Científicas (IBV-CSIC), Spain

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BMC Research Notes 2008, 1:5  doi:10.1186/1756-0500-1-5

Published: 28 February 2008



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.


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.


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.