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

Bohlin J, Skjerve E, Ussery DW - BMC Genomics (2008)

Bottom Line: The increasing number of sequenced prokaryotic genomes contains a wealth of genomic data that needs to be effectively analysed.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Norwegian School of Veterinary Science, P.O. Box 8146 Dep., N-0033 Oslo, Norway. n.bohlin@veths.no

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.

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Homology search/alignment based on heptanucleotide ROFs in Mycobacterium leprae. Homology search based on heptanucleotide ROFs in M. leprae, using a 1 kbp non-overlapping sliding window compared with a vector consisting of heptanucleotide frequencies taken from 5 kbp of T. maritima DNA consisting of 16S, 23S and 5S rRNA genes. The horizontal axis represents nucleotide positions, each point spanning 1 kbp, in the M. leprae chromosome, while the vertical axis gives correlation values based on comparisons between the sliding window and the T. maritima DNA vector. The marked peak indicates the closest hit, containing corresponding rRNA genes in M. leprae. Although M. leprae is very distantly related to T. maritima (hexanucleotide ZOM score of 0.13) its rRNA genes could be detected using DNA from the corresponding T. maritima rRNA genes with the search method based on ROFs.
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Figure 5: Homology search/alignment based on heptanucleotide ROFs in Mycobacterium leprae. Homology search based on heptanucleotide ROFs in M. leprae, using a 1 kbp non-overlapping sliding window compared with a vector consisting of heptanucleotide frequencies taken from 5 kbp of T. maritima DNA consisting of 16S, 23S and 5S rRNA genes. The horizontal axis represents nucleotide positions, each point spanning 1 kbp, in the M. leprae chromosome, while the vertical axis gives correlation values based on comparisons between the sliding window and the T. maritima DNA vector. The marked peak indicates the closest hit, containing corresponding rRNA genes in M. leprae. Although M. leprae is very distantly related to T. maritima (hexanucleotide ZOM score of 0.13) its rRNA genes could be detected using DNA from the corresponding T. maritima rRNA genes with the search method based on ROFs.

Mentions: For the distant homology search the heptanucleotide frequencies of a 5 kbp DNA sequence consisting of rRNA genes taken from T. maritima were compared against heptanucleotide frequencies in the M. leprae chromosome (hexanucleotide ZOM correlation 0.13 with T. maritima) with the sliding window approach described in the Methods section. From Figure 5, a good hit can be observed that achieved a noticeable higher correlation score around position 1.345 mbp than any other place in the genome. BLAST reports the corresponding DNA to be M. leprae 5S, 16S, 23S rRNA genes with a 100% identity score. The DNA taken from T. maritima obtained only a 75% identity score with the M. leprae genome, indicating that the ROF method can cope with both large and mutated DNA sequences, while still being fairly fast.


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

Bohlin J, Skjerve E, Ussery DW - BMC Genomics (2008)

Homology search/alignment based on heptanucleotide ROFs in Mycobacterium leprae. Homology search based on heptanucleotide ROFs in M. leprae, using a 1 kbp non-overlapping sliding window compared with a vector consisting of heptanucleotide frequencies taken from 5 kbp of T. maritima DNA consisting of 16S, 23S and 5S rRNA genes. The horizontal axis represents nucleotide positions, each point spanning 1 kbp, in the M. leprae chromosome, while the vertical axis gives correlation values based on comparisons between the sliding window and the T. maritima DNA vector. The marked peak indicates the closest hit, containing corresponding rRNA genes in M. leprae. Although M. leprae is very distantly related to T. maritima (hexanucleotide ZOM score of 0.13) its rRNA genes could be detected using DNA from the corresponding T. maritima rRNA genes with the search method based on ROFs.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2289816&req=5

Figure 5: Homology search/alignment based on heptanucleotide ROFs in Mycobacterium leprae. Homology search based on heptanucleotide ROFs in M. leprae, using a 1 kbp non-overlapping sliding window compared with a vector consisting of heptanucleotide frequencies taken from 5 kbp of T. maritima DNA consisting of 16S, 23S and 5S rRNA genes. The horizontal axis represents nucleotide positions, each point spanning 1 kbp, in the M. leprae chromosome, while the vertical axis gives correlation values based on comparisons between the sliding window and the T. maritima DNA vector. The marked peak indicates the closest hit, containing corresponding rRNA genes in M. leprae. Although M. leprae is very distantly related to T. maritima (hexanucleotide ZOM score of 0.13) its rRNA genes could be detected using DNA from the corresponding T. maritima rRNA genes with the search method based on ROFs.
Mentions: For the distant homology search the heptanucleotide frequencies of a 5 kbp DNA sequence consisting of rRNA genes taken from T. maritima were compared against heptanucleotide frequencies in the M. leprae chromosome (hexanucleotide ZOM correlation 0.13 with T. maritima) with the sliding window approach described in the Methods section. From Figure 5, a good hit can be observed that achieved a noticeable higher correlation score around position 1.345 mbp than any other place in the genome. BLAST reports the corresponding DNA to be M. leprae 5S, 16S, 23S rRNA genes with a 100% identity score. The DNA taken from T. maritima obtained only a 75% identity score with the M. leprae genome, indicating that the ROF method can cope with both large and mutated DNA sequences, while still being fairly fast.

Bottom Line: The increasing number of sequenced prokaryotic genomes contains a wealth of genomic data that needs to be effectively analysed.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.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.

View Article: PubMed Central - HTML - PubMed

Affiliation: Norwegian School of Veterinary Science, P.O. Box 8146 Dep., N-0033 Oslo, Norway. n.bohlin@veths.no

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.

Show MeSH
Related in: MedlinePlus