Fast comparison of DNA sequences by oligonucleotide profiling

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 t...

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Bibliographic Details
Published in:BMC research notes 2008-02, Vol.1 (1), p.5-5, Article 5
Main Authors: Arnau, Vicente, Gallach, Miguel, Marín, Ignacio
Format: Article
Language:English
Subjects:
Comparative analysis
DNA testing
Methods
Nucleotide sequence
Technical Note
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Summary: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
ISSN:1756-0500
1756-0500
DOI:10.1186/1756-0500-1-5