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Genome-wide DNA polymorphism analyses using VariScan.

Hutter S, Vilella AJ, Rozas J - BMC Bioinformatics (2006)

Bottom Line: Additionally, we have also incorporated a graphical-user interface.The main features of this software are: i) exhaustive population-genetic analyses including those based on the coalescent theory; ii) analysis adapted to the shallow data generated by the high-throughput genome projects; iii) use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv) identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v) visualization of the results integrated with current genome annotations in commonly available genome browsers.VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain. hutter@zi.biologie.uni-muenchen.de

ABSTRACT

Background: DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis.

Results: We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i) exhaustive population-genetic analyses including those based on the coalescent theory; ii) analysis adapted to the shallow data generated by the high-throughput genome projects; iii) use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv) identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v) visualization of the results integrated with current genome annotations in commonly available genome browsers.

Conclusion: VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.

Show MeSH
Visualization on the UCSC browser of the MRA analysis based on θ values from the mouse genome resequencing project data [20]. The USCS browser shows a 20 Mb-region (within positions 65.000,001–85,000,000). The first two tracks (customer tracks) represent the signal reconstruction of low-frequency bands with information from 9 to 11 MRA levels (first track), and from 12 to 16 MRA levels (second track).
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Figure 3: Visualization on the UCSC browser of the MRA analysis based on θ values from the mouse genome resequencing project data [20]. The USCS browser shows a 20 Mb-region (within positions 65.000,001–85,000,000). The first two tracks (customer tracks) represent the signal reconstruction of low-frequency bands with information from 9 to 11 MRA levels (first track), and from 12 to 16 MRA levels (second track).

Mentions: The SW and MRA results can easily be visualized in available genome browsers (see figure 3), such as the Human Genome Web Browser at UCSC [45] and any Web browser using Gbrowse [46]. This is accomplished by writing the relevant outcome in the so-called custom annotation track formats. In this way, the relevant results (profile of the haplotype or nucleotide diversity along the DNA sequence) can be visualized integrating available genome features (genes, repetitive or intergenic regions, etc).


Genome-wide DNA polymorphism analyses using VariScan.

Hutter S, Vilella AJ, Rozas J - BMC Bioinformatics (2006)

Visualization on the UCSC browser of the MRA analysis based on θ values from the mouse genome resequencing project data [20]. The USCS browser shows a 20 Mb-region (within positions 65.000,001–85,000,000). The first two tracks (customer tracks) represent the signal reconstruction of low-frequency bands with information from 9 to 11 MRA levels (first track), and from 12 to 16 MRA levels (second track).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC1574356&req=5

Figure 3: Visualization on the UCSC browser of the MRA analysis based on θ values from the mouse genome resequencing project data [20]. The USCS browser shows a 20 Mb-region (within positions 65.000,001–85,000,000). The first two tracks (customer tracks) represent the signal reconstruction of low-frequency bands with information from 9 to 11 MRA levels (first track), and from 12 to 16 MRA levels (second track).
Mentions: The SW and MRA results can easily be visualized in available genome browsers (see figure 3), such as the Human Genome Web Browser at UCSC [45] and any Web browser using Gbrowse [46]. This is accomplished by writing the relevant outcome in the so-called custom annotation track formats. In this way, the relevant results (profile of the haplotype or nucleotide diversity along the DNA sequence) can be visualized integrating available genome features (genes, repetitive or intergenic regions, etc).

Bottom Line: Additionally, we have also incorporated a graphical-user interface.The main features of this software are: i) exhaustive population-genetic analyses including those based on the coalescent theory; ii) analysis adapted to the shallow data generated by the high-throughput genome projects; iii) use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv) identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v) visualization of the results integrated with current genome annotations in commonly available genome browsers.VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms.

View Article: PubMed Central - HTML - PubMed

Affiliation: Departament de Genètica, Facultat de Biologia, Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain. hutter@zi.biologie.uni-muenchen.de

ABSTRACT

Background: DNA sequence polymorphisms analysis can provide valuable information on the evolutionary forces shaping nucleotide variation, and provides an insight into the functional significance of genomic regions. The recent ongoing genome projects will radically improve our capabilities to detect specific genomic regions shaped by natural selection. Current available methods and software, however, are unsatisfactory for such genome-wide analysis.

Results: We have developed methods for the analysis of DNA sequence polymorphisms at the genome-wide scale. These methods, which have been tested on a coalescent-simulated and actual data files from mouse and human, have been implemented in the VariScan software package version 2.0. Additionally, we have also incorporated a graphical-user interface. The main features of this software are: i) exhaustive population-genetic analyses including those based on the coalescent theory; ii) analysis adapted to the shallow data generated by the high-throughput genome projects; iii) use of genome annotations to conduct a comprehensive analyses separately for different functional regions; iv) identification of relevant genomic regions by the sliding-window and wavelet-multiresolution approaches; v) visualization of the results integrated with current genome annotations in commonly available genome browsers.

Conclusion: VariScan is a powerful and flexible suite of software for the analysis of DNA polymorphisms. The current version implements new algorithms, methods, and capabilities, providing an important tool for an exhaustive exploratory analysis of genome-wide DNA polymorphism data.

Show MeSH