| 1. |
- Dalevi, Daniel, 1974, et al.
(författare)
-
Bayesian classifiers for detecting HGT using fixed and variable order Markov models of genomic signatures
- 2006
-
Ingår i: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 22:5, s. 517-522
-
Tidskriftsartikel (refereegranskat)abstract
- Analyses of genomic signatures are gaining attention as they allow studies of species-specific relationships without involving alignments of homologous sequences. A naïve Bayesian classifier was built to discriminate between different bacterial compositions of short oligomers, also known as DNA words. The classifier has proven successful in identifying foreign genes in Neisseria meningitis. In this study we extend the classifier approach using either a fixed higher order Markov model (Mk) or a variable length Markov model (VLMk).
|
|
| 2. |
- Dalevi, Daniel, 1974, et al.
(författare)
-
Expected Gene Order Distances and Model Selection in Bacteria
- 2008
-
Ingår i: Bioinformatics. - Oxford, United Kingdom : Oxford University Press. - 1367-4803 .- 1367-4811. ; 24:11, s. 1332-1338
-
Tidskriftsartikel (refereegranskat)abstract
- Motivation: The evolutionary distance inferred from gene-order comparisons of related bacteria is dependent on the model. Therefore, it is highly important to establish reliable assumptions before inferring its magnitude. Results: We investigate the patterns of dotplots between species of bacteria with the purpose of model selection in gene-order problems. We find several categories of data which can be explained by carefully weighing the contributions of reversals, transpositions, symmetrical reversals, single gene transpositions and single gene reversals. We also derive method of moments distance estimates for some previously uncomputed cases, such as symmetrical reversals, single gene reversals and their combinations, as well as the single gene transpositions edit distance.
|
|
| 3. |
- Kristiansson, Erik, 1978, et al.
(författare)
-
ShotgunFunctionalizeR: an R-package for functional comparison of metagenomes
- 2009
-
Ingår i: Bioinformatics. - 1367-4803 .- 1367-4811. ; 25:20, s. 2737-2738
-
Tidskriftsartikel (refereegranskat)abstract
- Summary: Microorganisms are ubiquitous in nature and constitute intrinsic parts of almost every ecosystem. A culture-independent and powerful way to study microbial communities is metagenomics. In such studies, functional analysis is performed on fragmented genetic material from multiple species in the community. The recent advances in high-throughput sequencing have greatly increased the amount of data in metagenomic projects. At present, there is an urgent need for efficient statistical tools to analyse these data. We have created ShotgunFunctionalizeR, an R-package for functional comparison of metagenomes. The package contains tools for importing, annotating and visualizing metagenomic data produced by shotgun high-throughput sequencing. ShotgunFunctionalizeR contains several statistical procedures for assessing functional differences between samples, both for individual genes and for entire pathways. In addition to standard and previously published methods, we have developed and implemented a novel approach based on a Poisson model. This procedure is highly flexible and thus applicable to a wide range of different experimental designs. We demonstrate the potential of ShotgunFunctionalizeR by performing a regression analysis on metagenomes sampled at multiple depths in the Pacific Ocean.
|
|
