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A SNP-centric database for the investigation of the human genome.

Riva A, Kohane IS - BMC Bioinformatics (2004)

Bottom Line: It provides a rich local database generated by combining SNP data with the Human Genome sequence and with several other data sources, and offers the user a variety of querying, visualization and data export tools.The rich annotation database and the powerful data manipulation and presentation facilities it offers make SNPper a very useful online resource for SNP research.Its success proves the great need for integrated and interoperable resources in the field of computational biology, and shows how such systems may play a critical role in supporting the large-scale computational analysis of our genome.

View Article: PubMed Central - HTML - PubMed

Affiliation: Children's Hospital Informatics Program, Children's Hospital Boston, 320 Longwood, Avenue, Boston, MA 02115, USA. alberto.riva@tch.harvard.edu

ABSTRACT

Background: Single Nucleotide Polymorphisms (SNPs) are an increasingly important tool for genetic and biomedical research. Although current genomic databases contain information on several million SNPs and are growing at a very fast rate, the true value of a SNP in this context is a function of the quality of the annotations that characterize it. Retrieving and analyzing such data for a large number of SNPs often represents a major bottleneck in the design of large-scale association studies.

Description: SNPper is a web-based application designed to facilitate the retrieval and use of human SNPs for high-throughput research purposes. It provides a rich local database generated by combining SNP data with the Human Genome sequence and with several other data sources, and offers the user a variety of querying, visualization and data export tools. In this paper we describe the structure and organization of the SNPper database, we review the available data export and visualization options, and we describe how the architecture of SNPper and its specialized data structures support high-volume SNP analysis.

Conclusions: The rich annotation database and the powerful data manipulation and presentation facilities it offers make SNPper a very useful online resource for SNP research. Its success proves the great need for integrated and interoperable resources in the field of computational biology, and shows how such systems may play a critical role in supporting the large-scale computational analysis of our genome.

Show MeSH
Graphical representation of a gene with the SNPs it contains. The picture shows the output of a Java applet displaying the gene structure (exons are in blue, introns in gray) and all SNPs in the same region (represented by dots or squares). The user may scroll or zoom the display using the supplied buttons, or recenter the display by clicking on the top portion of the picture. Clicking on a SNP opens a pop-up window containing information about it.
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Figure 3: Graphical representation of a gene with the SNPs it contains. The picture shows the output of a Java applet displaying the gene structure (exons are in blue, introns in gray) and all SNPs in the same region (represented by dots or squares). The user may scroll or zoom the display using the supplied buttons, or recenter the display by clicking on the top portion of the picture. Clicking on a SNP opens a pop-up window containing information about it.

Mentions: Finally, Figure 3 shows the output of a Java applet that can be used to display SNPsets in graphical form. The structure of the gene is shown using bars of different colors and thickness; SNPs are identified by squares (if frequency information is available) or circles (otherwise), and are colored in green if validated, black otherwise. The applet provides commands to scroll the display left or right, and to zoom the display in or out.


A SNP-centric database for the investigation of the human genome.

Riva A, Kohane IS - BMC Bioinformatics (2004)

Graphical representation of a gene with the SNPs it contains. The picture shows the output of a Java applet displaying the gene structure (exons are in blue, introns in gray) and all SNPs in the same region (represented by dots or squares). The user may scroll or zoom the display using the supplied buttons, or recenter the display by clicking on the top portion of the picture. Clicking on a SNP opens a pop-up window containing information about it.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC395999&req=5

Figure 3: Graphical representation of a gene with the SNPs it contains. The picture shows the output of a Java applet displaying the gene structure (exons are in blue, introns in gray) and all SNPs in the same region (represented by dots or squares). The user may scroll or zoom the display using the supplied buttons, or recenter the display by clicking on the top portion of the picture. Clicking on a SNP opens a pop-up window containing information about it.
Mentions: Finally, Figure 3 shows the output of a Java applet that can be used to display SNPsets in graphical form. The structure of the gene is shown using bars of different colors and thickness; SNPs are identified by squares (if frequency information is available) or circles (otherwise), and are colored in green if validated, black otherwise. The applet provides commands to scroll the display left or right, and to zoom the display in or out.

Bottom Line: It provides a rich local database generated by combining SNP data with the Human Genome sequence and with several other data sources, and offers the user a variety of querying, visualization and data export tools.The rich annotation database and the powerful data manipulation and presentation facilities it offers make SNPper a very useful online resource for SNP research.Its success proves the great need for integrated and interoperable resources in the field of computational biology, and shows how such systems may play a critical role in supporting the large-scale computational analysis of our genome.

View Article: PubMed Central - HTML - PubMed

Affiliation: Children's Hospital Informatics Program, Children's Hospital Boston, 320 Longwood, Avenue, Boston, MA 02115, USA. alberto.riva@tch.harvard.edu

ABSTRACT

Background: Single Nucleotide Polymorphisms (SNPs) are an increasingly important tool for genetic and biomedical research. Although current genomic databases contain information on several million SNPs and are growing at a very fast rate, the true value of a SNP in this context is a function of the quality of the annotations that characterize it. Retrieving and analyzing such data for a large number of SNPs often represents a major bottleneck in the design of large-scale association studies.

Description: SNPper is a web-based application designed to facilitate the retrieval and use of human SNPs for high-throughput research purposes. It provides a rich local database generated by combining SNP data with the Human Genome sequence and with several other data sources, and offers the user a variety of querying, visualization and data export tools. In this paper we describe the structure and organization of the SNPper database, we review the available data export and visualization options, and we describe how the architecture of SNPper and its specialized data structures support high-volume SNP analysis.

Conclusions: The rich annotation database and the powerful data manipulation and presentation facilities it offers make SNPper a very useful online resource for SNP research. Its success proves the great need for integrated and interoperable resources in the field of computational biology, and shows how such systems may play a critical role in supporting the large-scale computational analysis of our genome.

Show MeSH