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LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources
2005
Bioinformatics
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Results: We have developed LS-SNP, a genomic scale software pipeline to annotate nsSNPs. ...
Availability: http://www.salilab.org/LS-SNP Contact: rachelk@salilab.org Supplementary information: http://salilab.org/LS-SNP/supp-info.pdf ...
The functional annotation is based on a variety of information sources brought together through LS-SNP that might not be convincing individually (comparative structure model with 51% target-template sequence ...
doi:10.1093/bioinformatics/bti442
pmid:15827081
fatcat:vdfuvxosjjg25eljpouakufypm
PolyDoms: a whole genome database for the identification of non-synonymous coding SNPs with the potential to impact disease
2007
Nucleic Acids Research
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This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial ...
Conflict of interest statement. None declared. ...
(C) Tabular description of nsSNP predictions based on PolyPhen and SIFT analysis and LS-SNP annotations (refer to B above for descriptions of color codes). ...
doi:10.1093/nar/gkl826
pmid:17142238
pmcid:PMC1669724
fatcat:veb5ubbjfbhifhmfhxv7vimxeu
MODBASE: a database of annotated comparative protein structure models and associated resources
2006
Nucleic Acids Research
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LS-SNP, http://salilab.org/LS-SNP). ...
MODBASE (http://salilab.org/modbase) is a database of annotated comparative protein structure models for all available protein sequences that can be matched to at least one known protein structure. ...
LS-SNP LS-SNP (http://www.salilab.org/LS-SNP) (31) is a database of annotated single nucleotide polymorphisms in human protein-coding exons that result in a changed amino acid residue type (non-synonymous ...
doi:10.1093/nar/gkj059
pmid:16381869
pmcid:PMC1347422
fatcat:quimgf3kibesrcsogatfoeizp4
Next generation tools for the annotation of human SNPs
2009
Briefings in Bioinformatics
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Many tools today produce results that are difficult to understand without bioinformatics expertise, are biased towards non-synonymous SNPs, and do not necessarily reflect up-to-date versions of their source ...
Computational biology has the opportunity to play an important role in the identification of functional single nucleotide polymorphisms (SNPs) discovered in large-scale genotyping studies, ultimately yielding ...
Figure 2 : 2 Trends in scope of SNP webservers. (a) Prior to 2006, protein-based servers that only handle non-synonymous SNPs were predominant. ...
doi:10.1093/bib/bbn047
pmid:19181721
pmcid:PMC2638621
fatcat:wrxufl5ayvd2nc7v5x3a4d3dr4
Genome bioinformatic analysis of nonsynonymous SNPs
2007
BMC Bioinformatics
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A proportion of these will alter protein sequences, the most common of which is the non-synonymous single nucleotide polymorphism (nsSNP). ...
The nsSNP information came from two sources, the OMIM database which are rare (minor allele frequency, MAF, < 0.01) and are known to cause penetrant, monogenic diseases. ...
-M.P. was supported by a grant from the Spanish Ministry of Education and Science. ...
doi:10.1186/1471-2105-8-301
pmid:17708757
pmcid:PMC1978506
fatcat:ylrs3tjgfbaqdpjb4bsms6xte4
Analytical methods for inferring functional effects of single base pair substitutions in human cancers
2009
Human Genetics
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Frequency-based methods identify the most highly mutated genes in large-scale cancer sequencing eVorts while bioinformatics approaches are eVective for independent evaluation of both non-synonymous mutations ...
We also review current knowledge and tools that can be utilized for analysis of alterations in non-protein-coding genomic sequence. ...
the original author(s) and source are credited. ...
doi:10.1007/s00439-009-0677-y
pmid:19434427
pmcid:PMC2762536
fatcat:7clebx3wujd2bikfnedghiu7we
Leucine to proline substitution by SNP at position 197 in Caspase-9 gene expression leads to neuroblastoma: a bioinformatics analysis
2012
3 Biotech
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To determine whether a non-synonymous SNP (nsSNP) in this gene affects its protein product, we used certain computational tools which predicted one nsSNP, rs1052574, to have deleterious phenotypic effect ...
This can help us understand the genetic variations that can alter the function of the gene products. A total of 941 SNPs are investigated for CASP9 gene. ...
and the source are credited. ...
doi:10.1007/s13205-012-0088-y
pmid:28324374
pmcid:PMC3646108
fatcat:br3s5iy3pjgwhdkafhp7gfq5cm
Bioinformatics for personal genome interpretation
2012
Briefings in Bioinformatics
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This information has enabled researchers to develop bioinformatics tools to analyze the rapidly increasing amount of newly extracted variation data and to predict the effect of uncharacterized variants ...
Thus, a major current effort of the scientific community focuses on evaluating individual predispositions to specific phenotypic traits given their genetic backgrounds. ...
Acknowledgements We acknowledge all the colleagues who contributed in the organization and panel discussions at the last PSB and ISMB SNP-SIG meetings. ...
doi:10.1093/bib/bbr070
pmid:22247263
pmcid:PMC3404395
fatcat:zdu5z4bbtncerp7cyw6mjrf3d4
GRASP: analysis of genotype-phenotype results from 1390 genome-wide association studies and corresponding open access database
2014
Bioinformatics
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We re-annotated GWAS results with 16 annotation sources including some rarely compared to GWAS results (e.g. RNAediting sites, lincRNAs, PTMs). ...
We created a deeply extracted and annotated database of genome-wide association studies (GWAS) results. GRASP v1.0 contains 46.2 million SNP-phenotype association from among 1390 GWAS studies. ...
, clinical annotation in dbSNP and for non-synonymous SNPs, where available, PolyPhen2, SIFT and LS-SNP prediction results. ...
doi:10.1093/bioinformatics/btu273
pmid:24931982
pmcid:PMC4072913
fatcat:acu3llu625dkpjyz6nezyzljau
Modeling and analyzing three-dimensional structures of human disease proteins
2006
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing
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In contrast, the non-synonymous SNPs appear to be randomly distributed on the surface. ...
With the help of information on disease-related mutations, they can also show us how they malfunction in diseases. ...
cause changes of amino acids in the protein product of a gene (i.e., non-synonymous SNPs, nsSNPs) [1] . ...
pmid:17094259
fatcat:prl3niulqrc3dhsomhmrjw6fvy
Interpretation of the Consequences of Mutations in Protein Kinases: Combined Use of Bioinformatics and Text Mining
2012
Frontiers in Physiology
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In particular we will focus on the problem of benchmarking the predictions with independent gold standard datasets. ...
Finally, we will discuss how text mining approaches constitute a powerful tool for the interpretation of the consequences of mutations in the context of disease genome analysis with particular focus on ...
www.bioinf.org.uk/saap/db/
SNPeffect 2.0 (Reumers et al.,
2006)
A database mapping molecular phenotypic effects of
human non-synonymous coding SNPs
http://snpeffect.switchlab.org
ModBase (Pieper ...
doi:10.3389/fphys.2012.00323
pmid:23055974
pmcid:PMC3449330
fatcat:i2qqkuh4nfde3pxeknjbvgpfpe
Pathogenicity prediction of non-synonymous single nucleotide variants in dilated cardiomyopathy
2015
Briefings in Bioinformatics
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Non-synonymous single nucleotide variants (nsSNVs) in coding DNA regions can result in phenotypic differences between individuals; however, only some nsSNVs are causative for a certain disease. ...
Most tools rely mainly on sequence features; beyond these, structural information is important to analyze the relationship of nsSNVs with disease phenotypes. ...
In addition, we also tested SNPEffect [18] , nsSNP Analyzer [19] and LS-SNP [20] , but these prediction methods are not suitable for large-scale studies or require prerequisites that are not generally ...
doi:10.1093/bib/bbu054
pmid:25638801
fatcat:3n5ktqmvgnfjjoke5v5m4orajq
Analysis of genetic variation and potential applications in genome-scale metabolic modeling
2015
Frontiers in Bioengineering and Biotechnology
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In this article, we review challenges in the integration and analysis of large-scale re-sequencing data, present an extensive overview of bioinformatics methods for predicting the effects of genetic variants ...
on protein function, and discuss approaches for interfacing existing bioinformatics approaches with genome-scale models of cellular processes in order to predict effects of sequence variation on cellular ...
It predicts non-synonymous SNPs. ...
doi:10.3389/fbioe.2015.00013
pmid:25763369
pmcid:PMC4329917
fatcat:jbh3kw2q5rclviw6tm6quqi5ie
SNPLogic: an interactive single nucleotide polymorphism selection, annotation, and prioritization system
2008
Nucleic Acids Research
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SNPLogic (http://www.snplogic.org) brings together single nucleotide polymorphism (SNP) information from numerous sources to provide a comprehensive SNP selection, annotation and prioritization system ...
We have found integration of SNP annotation in the context of pathway information and functional prediction scores to be a powerful approach to the analysis and interpretation of SNP-disease association ...
For example, we performed pathway-based analyses on adult glioma using a panel of 10,000 non-synonymous SNPs (1). ...
doi:10.1093/nar/gkn756
pmid:18984625
pmcid:PMC2686434
fatcat:mgckpbqx5bbsbmycxcl66sxzb4
SPOT: a web-based tool for using biological databases to prioritize SNPs after a genome-wide association study
2010
Nucleic Acids Research
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Investigators will often incorporate information from biological databases so that biologically relevant SNPs, such as those in genes related to the phenotype or with potentially nonneutral effects on ...
The SPOT web site allows users to upload a list of SNPs and GWAS P-values and returns a prioritized list of SNPs using the GIN method. ...
Conflict of interest statement. None declared. ...
doi:10.1093/nar/gkq513
pmid:20529875
pmcid:PMC2896195
fatcat:crtot5o3rrc5jgsbuzlf623gpq
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