Fast comparison of DNA sequences by oligonucleotide profiling.

BMC Research Notes
Vicente ArnauI Marín

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. 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 th...Continue Reading

References

Apr 25, 1990·Nucleic Acids Research·H J Jeffrey
Apr 1, 1998·Bioinformatics·S LevyG D Stormo
Dec 10, 1998·Genome Research·A BrazmaE Ukkonen
Feb 3, 1999·Annual Review of Genetics·S KarlinJ Mrázek
Oct 25, 2001·Journal of Molecular Evolution·C Shioiri, N Takahata
Apr 5, 2002·Genome Research·W James Kent
Jul 11, 2002·Proceedings of the National Academy of Sciences of the United States of America·Mark RebeizJames W Posakony
Oct 5, 2002·Nucleic Acids Research·Jan MrázekSamuel Karlin
Dec 20, 2002·Nucleic Acids Research·Saurabh Sinha, Martin Tompa
Mar 4, 2003·Bioinformatics·Susana Vinga, Jonas Almeida
Sep 17, 2003·Genome Research·John HealyMichael Wigler
Feb 14, 2004·Nucleic Acids Research·Leonardo Mariño-RamírezDavid Landsman
Jun 25, 2005·BMC Bioinformatics·Per StenbergJan Larsson
Jun 28, 2005·Nucleic Acids Research·Bernard FertilAlain Giron
Nov 13, 2007·BMC Genomics·Miguel GallachIgnacio Marín

❮ Previous
Next ❯

Citations

Nov 13, 2007·BMC Genomics·Miguel GallachIgnacio Marín
May 23, 2014·Genome Biology and Evolution·Miguel Gallach
Aug 2, 2013·Briefings in Bioinformatics·Oliver Bonham-CarterDhundy Bastola
Jan 10, 2012·Journal of Theoretical Biology·Michael HackenbergJosé L Oliver
Nov 22, 2011·Clinical Chemistry·Shengnan JinChunming Ding

❮ Previous
Next ❯

Software Mentioned

Linux
UVWORD
BLAST
Windows

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.