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Updated: Jul 2, 2026
08:04
DNA Sequence Recognition by DNA Primase Using High-Throughput Primase Profiling
Published on: October 8, 2019
Fast comparison of DNA sequences by oligonucleotide profiling
Vicente Arnau1, Miguel Gallach, Ignacio Marín
1Departmento de Informática. Universidad de Valencia, Spain. vicente@arnau@uv.es
BMC Research Notes
|August 20, 2008
Summary
UVWORD is a new program for DNA sequence analysis that rapidly identifies oligonucleotide patterns. This tool enables novel genomic screenings by analyzing DNA words up to 14 nucleotides long.
Area of Science:
- Genomics
- Bioinformatics
- Computational Biology
Background:
- DNA sequence comparison is a fundamental challenge in genomics.
- Advancements in personal computing enable sophisticated bioinformatics analyses.
- Novel strategies for DNA sequence analysis are emerging.
Purpose of the Study:
- To introduce UVWORD, a novel program for DNA sequence analysis.
- To enable rapid identification and counting of DNA words (oligonucleotides) within sequences.
- To facilitate new types of genomic screenings.
Main Methods:
- Oligonucleotide profiling: counting occurrences of DNA words in a target sequence within a source sequence.
- Analysis of DNA words ranging from k=1 to k=14 nucleotides.
- Calculation of average counts for contiguous word groups.
Main Results:
- UVWORD achieves analysis speeds of 3.4 to 16 million words per second on standard computers.
- The program efficiently screens even very long DNA molecules.
- It allows analysis of rare, long DNA words (up to 14 nucleotides).
Conclusions:
- UVWORD offers novel screening capabilities complementary to existing tools like BLAST.
- The method facilitates determination of oligonucleotide content and repetitive sequence distribution.
- Applications include analyzing evolutionary sequence conservation and identifying similar DNA regions across genomes.
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