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LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources

R. Karchin, M. Diekhans, L. Kelly, D. J. Thomas, U. Pieper, N. Eswar, D. Haussler, A. Sali
2005 Bioinformatics  
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

A. G. Jegga, S. Gowrisankar, J. Chen, B. J. Aronow
2007 Nucleic Acids Research  
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

U. Pieper
2006 Nucleic Acids Research  
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

Rachel Karchin
2009 Briefings in Bioinformatics  
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

David F Burke, Catherine L Worth, Eva-Maria Priego, Tammy Cheng, Luc J Smink, John A Todd, Tom L Blundell
2007 BMC Bioinformatics  
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

William Lee, Peng Yue, Zemin Zhang
2009 Human Genetics  
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

Arpita Kundu, Susmita Bag, Sudha Ramaiah, Anand Anbarasu
2012 3 Biotech  
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

E. Capriotti, N. L. Nehrt, M. G. Kann, Y. Bromberg
2012 Briefings in Bioinformatics  
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

R. Leslie, C. J. O'Donnell, A. D. Johnson
2014 Bioinformatics  
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

Yuzhen Ye, Zhanwen Li, Adam Godzik
2006 Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing  
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

Jose M. G. Izarzugaza, Martin Krallinger, Alfonso Valencia
2012 Frontiers in Physiology  
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

Sabine C. Mueller, Christina Backes, Jan Haas, Hugo A. Katus, Benjamin Meder, Eckart Meese, Andreas Keller
2015 Briefings in Bioinformatics  
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

João Cardoso
2015 Frontiers in Bioengineering and Biotechnology  
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

Alexander R. Pico, Ivan V. Smirnov, Jeffrey S. Chang, Ru-Fang Yeh, Joseph L. Wiemels, John K. Wiencke, Tarik Tihan, Bruce R. Conklin, Margaret Wrensch
2008 Nucleic Acids Research  
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

S. F. Saccone, R. Bolze, P. Thomas, J. Quan, G. Mehta, E. Deelman, J. A. Tischfield, J. P. Rice
2010 Nucleic Acids Research  
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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