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MutDB: update on development of tools for the biochemical analysis of genetic variation.

Singh A, Olowoyeye A, Baenziger PH, Dantzer J, Kann MG, Radivojac P, Heiland R, Mooney SD - Nucleic Acids Res. (2007)

Bottom Line: Understanding how genetic variation affects the molecular function of gene products is an emergent area of bioinformatic research.Though these functional annotations are mainly focused on nonsynonymous SNPs, some information on other SNP types included in dbSNP is also provided.Additionally, we have developed a new functionality that facilitates KEGG pathway visualization of genes containing SNPs and a SNP query tool for visualizing and exporting sets of SNPs that share selected features based on certain filters.

View Article: PubMed Central - PubMed

Affiliation: Center for Computational Biology and Bioinfomatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, 410 W. 10th Street, Suite 5000, Indianapolis, IN 46202, USA.

ABSTRACT
Understanding how genetic variation affects the molecular function of gene products is an emergent area of bioinformatic research. Here, we present updates to MutDB (http://www.mutdb.org), a tool aiming to aid bioinformatic studies by integrating publicly available databases of human genetic variation with molecular features and clinical phenotype data. MutDB, first developed in 2002, integrates annotated SNPs in dbSNP and amino acid substitutions in Swiss-Prot with protein structural information, links to scores that predict functional disruption and other useful annotations. Though these functional annotations are mainly focused on nonsynonymous SNPs, some information on other SNP types included in dbSNP is also provided. Additionally, we have developed a new functionality that facilitates KEGG pathway visualization of genes containing SNPs and a SNP query tool for visualizing and exporting sets of SNPs that share selected features based on certain filters.

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SNP query tool snapshot highlighting SNP filtering. Multiple filtering options include: validation (T/F), HapMap (31) (T/F), Location, avHet, avHetSE, HapMap Frequency (CEU, CHB, JPT, YRI), SIFT score and UCSC conservation. Users can preview current filtering criteria by scrolling over pop-up window link. Once SNPs are selected, Haploview like images can be rendered showing HapMap LD structure (lower right).
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Figure 1: SNP query tool snapshot highlighting SNP filtering. Multiple filtering options include: validation (T/F), HapMap (31) (T/F), Location, avHet, avHetSE, HapMap Frequency (CEU, CHB, JPT, YRI), SIFT score and UCSC conservation. Users can preview current filtering criteria by scrolling over pop-up window link. Once SNPs are selected, Haploview like images can be rendered showing HapMap LD structure (lower right).

Mentions: In addition to updating to the latest mutation and SNP datasets, here we present several additions to the MutDB resource. First, we have developed a pathway visualization add-on to MutDB that leads the biologist from mutations in a gene to KEGG (23) biological pathways involving the gene. This enables the researcher to view the systems context of both a mutation and its associated phenotype. Second, we have constructed an AJAX (Asynchronous JavaScript and XML) based SNP query tool that allows users to save searches, view Haploview-like haplotype structure (24), and select subsets of SNPs based on frequencies and SNP scores. Together these tools represent a useful addition to our existing library of genetic research tools (Figure 1).Figure 1.


MutDB: update on development of tools for the biochemical analysis of genetic variation.

Singh A, Olowoyeye A, Baenziger PH, Dantzer J, Kann MG, Radivojac P, Heiland R, Mooney SD - Nucleic Acids Res. (2007)

SNP query tool snapshot highlighting SNP filtering. Multiple filtering options include: validation (T/F), HapMap (31) (T/F), Location, avHet, avHetSE, HapMap Frequency (CEU, CHB, JPT, YRI), SIFT score and UCSC conservation. Users can preview current filtering criteria by scrolling over pop-up window link. Once SNPs are selected, Haploview like images can be rendered showing HapMap LD structure (lower right).
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2238958&req=5

Figure 1: SNP query tool snapshot highlighting SNP filtering. Multiple filtering options include: validation (T/F), HapMap (31) (T/F), Location, avHet, avHetSE, HapMap Frequency (CEU, CHB, JPT, YRI), SIFT score and UCSC conservation. Users can preview current filtering criteria by scrolling over pop-up window link. Once SNPs are selected, Haploview like images can be rendered showing HapMap LD structure (lower right).
Mentions: In addition to updating to the latest mutation and SNP datasets, here we present several additions to the MutDB resource. First, we have developed a pathway visualization add-on to MutDB that leads the biologist from mutations in a gene to KEGG (23) biological pathways involving the gene. This enables the researcher to view the systems context of both a mutation and its associated phenotype. Second, we have constructed an AJAX (Asynchronous JavaScript and XML) based SNP query tool that allows users to save searches, view Haploview-like haplotype structure (24), and select subsets of SNPs based on frequencies and SNP scores. Together these tools represent a useful addition to our existing library of genetic research tools (Figure 1).Figure 1.

Bottom Line: Understanding how genetic variation affects the molecular function of gene products is an emergent area of bioinformatic research.Though these functional annotations are mainly focused on nonsynonymous SNPs, some information on other SNP types included in dbSNP is also provided.Additionally, we have developed a new functionality that facilitates KEGG pathway visualization of genes containing SNPs and a SNP query tool for visualizing and exporting sets of SNPs that share selected features based on certain filters.

View Article: PubMed Central - PubMed

Affiliation: Center for Computational Biology and Bioinfomatics, Department of Medical and Molecular Genetics, Indiana University School of Medicine, 410 W. 10th Street, Suite 5000, Indianapolis, IN 46202, USA.

ABSTRACT
Understanding how genetic variation affects the molecular function of gene products is an emergent area of bioinformatic research. Here, we present updates to MutDB (http://www.mutdb.org), a tool aiming to aid bioinformatic studies by integrating publicly available databases of human genetic variation with molecular features and clinical phenotype data. MutDB, first developed in 2002, integrates annotated SNPs in dbSNP and amino acid substitutions in Swiss-Prot with protein structural information, links to scores that predict functional disruption and other useful annotations. Though these functional annotations are mainly focused on nonsynonymous SNPs, some information on other SNP types included in dbSNP is also provided. Additionally, we have developed a new functionality that facilitates KEGG pathway visualization of genes containing SNPs and a SNP query tool for visualizing and exporting sets of SNPs that share selected features based on certain filters.

Show MeSH