Fast comparison of DNA sequences by oligonucleotide profiling.

ABSTRACT:

Background

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

SUBMITTER: Arnau V 

PROVIDER: S-EPMC2518268 | biostudies-literature | 2008 Feb

REPOSITORIES: biostudies-literature