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Quantitative frame analysis and the annotation of GC-rich (and other) prokaryotic genomes. An application to Anaeromyxobacter dehalogenans.

Oden S, Brocchieri L - Bioinformatics (2015)

Bottom Line: Graphical representations of contrasts in GC usage among codon frame positions (frame analysis) provide evidence of genes missing from the annotations of prokaryotic genomes of high GC content but the qualitative approach of visual frame analysis prevents its applicability on a genomic scale.We developed two quantitative methods for the identification and statistical characterization in sequence regions of three-base periodicity (hits) associated with open reading frame structures.We applied the NPACT procedures to two recently annotated strains of the deltaproteobacterium Anaeromyxobacter dehalogenans, identifying in both genomes numerous conserved ORFs not included in the published annotation of coding regions.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA and Genetics Institute, University of Florida, Gainesville, FL 32610, USA.

No MeSH data available.


Related in: MedlinePlus

Conservation of newly identified ORFs of four levels of ‘quality’ determined based on visual analysis of S-profiles, hits, and of ORF positional relation with neighboring genes (best: ***; good: **; possible: *; dubious: -). ORFs are characterized by the ‘Number of predictors’ (0 to 4) supporting their coding potential
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btv339-F4: Conservation of newly identified ORFs of four levels of ‘quality’ determined based on visual analysis of S-profiles, hits, and of ORF positional relation with neighboring genes (best: ***; good: **; possible: *; dubious: -). ORFs are characterized by the ‘Number of predictors’ (0 to 4) supporting their coding potential

Mentions: Virtually all ORFs conserved across genera and phyla, as well as those conserved between Anaeromyxobacter species or strains, showed best (***) or good (**) visual quality, and among these most were confirmed by the majority of gene predictors (Fig. 4). These results suggested that visual assessments of quality based on compositional contrast and position are reliable indicators of the coding capacity of an ORF, as supported by conservation and/or computational prediction, and thus of the level of confidence in the prediction. Furthermore, positional and compositional quality as well as gene-prediction, mutually supported many potential genes that could otherwise be excluded based on their lack of or limited conservation (Fig. 4 and Supplementary Tables S18–S21).Fig. 4.


Quantitative frame analysis and the annotation of GC-rich (and other) prokaryotic genomes. An application to Anaeromyxobacter dehalogenans.

Oden S, Brocchieri L - Bioinformatics (2015)

Conservation of newly identified ORFs of four levels of ‘quality’ determined based on visual analysis of S-profiles, hits, and of ORF positional relation with neighboring genes (best: ***; good: **; possible: *; dubious: -). ORFs are characterized by the ‘Number of predictors’ (0 to 4) supporting their coding potential
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4595893&req=5

btv339-F4: Conservation of newly identified ORFs of four levels of ‘quality’ determined based on visual analysis of S-profiles, hits, and of ORF positional relation with neighboring genes (best: ***; good: **; possible: *; dubious: -). ORFs are characterized by the ‘Number of predictors’ (0 to 4) supporting their coding potential
Mentions: Virtually all ORFs conserved across genera and phyla, as well as those conserved between Anaeromyxobacter species or strains, showed best (***) or good (**) visual quality, and among these most were confirmed by the majority of gene predictors (Fig. 4). These results suggested that visual assessments of quality based on compositional contrast and position are reliable indicators of the coding capacity of an ORF, as supported by conservation and/or computational prediction, and thus of the level of confidence in the prediction. Furthermore, positional and compositional quality as well as gene-prediction, mutually supported many potential genes that could otherwise be excluded based on their lack of or limited conservation (Fig. 4 and Supplementary Tables S18–S21).Fig. 4.

Bottom Line: Graphical representations of contrasts in GC usage among codon frame positions (frame analysis) provide evidence of genes missing from the annotations of prokaryotic genomes of high GC content but the qualitative approach of visual frame analysis prevents its applicability on a genomic scale.We developed two quantitative methods for the identification and statistical characterization in sequence regions of three-base periodicity (hits) associated with open reading frame structures.We applied the NPACT procedures to two recently annotated strains of the deltaproteobacterium Anaeromyxobacter dehalogenans, identifying in both genomes numerous conserved ORFs not included in the published annotation of coding regions.

View Article: PubMed Central - PubMed

Affiliation: Department of Molecular Genetics and Microbiology, University of Florida, Gainesville, FL 32610, USA and Genetics Institute, University of Florida, Gainesville, FL 32610, USA.

No MeSH data available.


Related in: MedlinePlus