TITLE

Reliability and applications of statistical methods based on oligonucleotide frequencies in bacterial and archaeal genomes

AUTHOR(S)
Bohlin, Jon; Skjerve, Eystein; Ussery, David W.
PUB. DATE
January 2008
SOURCE
BMC Genomics;2008, Vol. 9, Special section p1
SOURCE TYPE
Academic Journal
DOC. TYPE
Article
ABSTRACT
Background: The increasing number of sequenced prokaryotic genomes contains a wealth of genomic data that needs to be effectively analysed. A set of statistical tools exists for such analysis, but their strengths and weaknesses have not been fully explored. The statistical methods we are concerned with here are mainly used to examine similarities between archaeal and bacterial DNA from different genomes. These methods compare observed genomic frequencies of fixed-sized oligonucleotides with expected values, which can be determined by genomic nucleotide content, smaller oligonucleotide frequencies, or be based on specific statistical distributions. Advantages with these statistical methods include measurements of phylogenetic relationship with relatively small pieces of DNA sampled from almost anywhere within genomes, detection of foreign/ conserved DNA, and homology searches. Our aim was to explore the reliability and best suited applications for some popular methods, which include relative oligonucleotide frequencies (ROF), di- to hexanucleotide zero'th order Markov methods (ZOM) and 2.order Markov chain Method (MCM). Tests were performed on distant homology searches with large DNA sequences, detection of foreign/conserved DNA, and plasmid-host similarity comparisons. Additionally, the reliability of the methods was tested by comparing both real and random genomic DNA. Results: Our findings show that the optimal method is context dependent. ROFs were best suited for distant homology searches, whilst the hexanucleotide ZOM and MCM measures were more reliable measures in terms of phylogeny. The dinucleotide ZOM method produced high correlation values when used to compare real genomes to an artificially constructed random genome with similar %GC, and should therefore be used with care. The tetranucleotide ZOM measure was a good measure to detect horizontally transferred regions, and when used to compare the phylogenetic relationships between plasmids and hosts, significant correlation (R² = 0.4) was found with genomic GC content and intra-chromosomal homogeneity. Conclusion: The statistical methods examined are fast, easy to implement, and powerful for a number of different applications involving genomic sequence comparisons. However, none of the measures examined were superior in all tests, and therefore the choice of the statistical method should depend on the task at hand.
ACCESSION #
38122672

 

Related Articles

  • nhmmer: DNA homology search with profile HMMs. Wheeler, Travis J.; Eddy, Sean R. // Bioinformatics;Oct2013, Vol. 29 Issue 19, p2487 

    Summary: Sequence database searches are an essential part of molecular biology, providing information about the function and evolutionary history of proteins, RNA molecules and DNA sequence elements. We present a tool for DNA/DNA sequence comparison that is built on the HMMER framework, which...

  • Functional evolution of two subtly different (similar) folds. Agrawal, Vishal; Kishan, Radha K. V. // BMC Structural Biology;2001, Vol. 1, p5 

    Background: The function of proteins is a direct consequence of their three-dimensional structure. The structural classification of proteins describes the ways of folding patterns all proteins could adopt. Although, the protein folds were described in many ways the functional properties of...

  • Abundant Oligonucleotides Common to Most Bacteria. Davenport, Colin F.; Tümmler, Burkhard // PLoS ONE;2010, Vol. 5 Issue 3, p1 

    Background: Bacteria show a bias in their genomic oligonucleotide composition far beyond that dictated by G+C content. Patterns of over- and underrepresented oligonucleotides carry a phylogenetic signal and are thus diagnostic for individual species. Patterns of short oligomers have been...

  • Correlations Between Bacterial Ecology and Mobile DNA. Newton, Irene I. G.; Bordenstein, Seth R. // Current Microbiology;Jan2011, Vol. 62 Issue 1, p198 

    Several factors can affect the density of mobile DNA in bacterial genomes including rates of exposure to novel gene pools, recombination, and reductive evolution. These traits are difficult to measure across a broad range of bacterial species, but the ecological niches occupied by an organism...

  • Identification of the region in Escherichia coli DnaA protein required for specific recognition of the DnaA box. Yoshida, Y.; Obita, T.; Kokusho, Y.; Ohmura, T.; Katayama, T.; Ueda, T.; Imoto, T. // Cellular & Molecular Life Sciences;Sep2003, Vol. 60 Issue 9, p1998 

    DnaA protein binds specifically to a 9-base- pair motif called the DnaA box. Domain IV comprises 94 amino acid residues and is required for DNA binding. Using nuclear magnetic resonance analysis, we investigated the interaction between DnaA domain IV and both a DnaA box and a non-specific...

  • An Aromatic Sensor with Aversion to Damaged Strands Confers Versatility to DNA Repair. Maillard, Olivier; Solyom, Szilvia; Naegeli, Hanspeter // PLoS Biology;Apr2007, Vol. 5 Issue 4, p0717 

    It was not known how xeroderma pigmentosum group C (XPC) protein, the primary initiator of global nucleotide excision repair, achieves its outstanding substrate versatility. Here, we analyzed the molecular pathology of a unique Trp690Ser substitution, which is the only reported missense mutation...

  • First evidence of a retrotransposon-like element in olive (Olea europaea): implications in plant variety identification by SCAR-marker development. Hernández, P.; de la Rosa, R.; Rallo, L.; Martín, A.; Dorado, G. // Theoretical & Applied Genetics;May2001, Vol. 102 Issue 6/7, p1082 

    When developing SCARs by sequencing RAPD markers useful for olive variety identification, one RAPD sequence of 407 bp has been identified that shows significant DNA homology with more than 160 retrotransposon-like sequences. A generally coherent phylogenetic tree has been constructed based on...

  • Oligonucleotide Fingerprinting of Arrayed Genomic DNA Sequences Using LNA-Modified Hybridization Probes. Jian-Ping Liu; Drungowski, Mario; Nyarsik, Lajos; Schwartz, Regine; Lehrach, Hans; Herwig, Ralf; Janitz, Michal // Combinatorial Chemistry & High Throughput Screening;May2007, Vol. 10 Issue 4, p269 

    Recently, we established a robust method for the detection of hybridization events using a DNA microarray deposited on a nanoporous membrane. Here, in a follow-up study, we demonstrate the performance of this approach on a larger set of LNA-modified oligoprobes and genomic DNA sequences....

  • Identification of a new human DNA virus (TTV-like mini virus, TLMV) intermediately related to TT virus and chicken anemia virus. Takahashi, K.; Iwasa, Y.; Hijikata, M.; Mishiro, S. // Archives of Virology;May2000, Vol. 145 Issue 5, p979 

    Summary. TT virus (TTV) is the only known human virus with single-stranded circular DNA, with a possible but yet unclear relationship to chicken anemia virus (CAV) of the family Circoviridae. Here we report a new human virus resembling TTV and CAV, designated TTV-like mini virus (TLMV). This...

Share

Read the Article

Courtesy of THE LIBRARY OF VIRGINIA

Sorry, but this item is not currently available from your library.

Try another library?
Sign out of this library

Other Topics