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Next generation tools for the annotation of human SNPs

Rachel Karchin
<span title="">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
Here, I assess the utility of the current generation of webservers; and suggest improvements for the next generation of webservers to better deliver value to medical geneticists and molecular biologists  ...  It is the proportion of variability in a data set that is accounted for by a statistical model. Conserved A property of entities undergoing evolution.  ...  Acknowledgements The author thanks Dr Melissa Cline for valuable discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbn047">doi:10.1093/bib/bbn047</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19181721">pmid:19181721</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2638621/">pmcid:PMC2638621</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wrxufl5ayvd2nc7v5x3a4d3dr4">fatcat:wrxufl5ayvd2nc7v5x3a4d3dr4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190222205425/http://pdfs.semanticscholar.org/4372/b45be1670e5293f1829527eb9d6e3c47b823.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/43/72/4372b45be1670e5293f1829527eb9d6e3c47b823.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbn047"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2638621" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

MagicViewer: integrated solution for next-generation sequencing data visualization and genetic variation detection and annotation

H. Hou, F. Zhao, L. Zhou, E. Zhu, H. Teng, X. Li, Q. Bao, J. Wu, Z. Sun
<span title="2010-05-05">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
In conclusion, MagicViewer is a sophisticated assembly visualization and genetic variation annotation tool for next-generation sequencing data, which can be widely used in a variety of sequencing-based  ...  To satisfy the impending need for deciphering the large-scale data generated from next-generation sequencing, an integrated software MagicViewer is developed to easily visualize short read mapping, identify  ...  The GATK is a structured software library designed to enable rapid development of efficient and robust analysis tools for next-generation sequencing data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkq302">doi:10.1093/nar/gkq302</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20444865">pmid:20444865</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2896176/">pmcid:PMC2896176</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vckzrgfmlrcmbhullppt7utfja">fatcat:vckzrgfmlrcmbhullppt7utfja</a> </span>
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VDAP-GUI: a user-friendly pipeline for variant discovery and annotation of raw next-generation sequencing data

Ramesh Menon, Namrata V. Patel, Amitbikram Mohapatra, Chaitanya G. Joshi
<span title="2016-02-15">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/by5shwibsvfk3acyvniuab5bra" style="color: black;">3 Biotech</a> </i> &nbsp;
Even though next-generation sequencing (NGS) has become an invaluable tool in molecular biology, several laboratories with NGS facilities lack trained Bioinformaticians for data analysis.  ...  Here, focusing on the variant detection application of NGS analysis, we have developed a fully automated pipeline, namely Variant Discovery and Annotation Tool-Graphical User Interface (VDAP-GUI), which  ...  Acknowledgments The study was supported by Department of Biotechnology, Ministry of science and technology, India.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s13205-016-0382-1">doi:10.1007/s13205-016-0382-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28330138">pmid:28330138</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4754298/">pmcid:PMC4754298</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wsxqblo36bgcxbmmmzu7d5davm">fatcat:wsxqblo36bgcxbmmmzu7d5davm</a> </span>
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AnnTools: a comprehensive and versatile annotation toolkit for genomic variants

Vladimir Makarov, Tina O'Grady, Guiqing Cai, Jayon Lihm, Joseph D. Buxbaum, Seungtai Yoon
<span title="2012-01-18">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
AnnTools is a versatile bioinformatics application designed for comprehensive annotation of a full spectrum of human genome variation: novel and known single-nucleotide substitutions (SNP/SNV), short insertions  ...  The tool conveniently accepts user-provided tracks for custom annotation and offers flexibility in input data formats. The output is generated in the universal Variant Call Format.  ...  ACKNOWLEDGEMENTS We thank Dr Violetta Barbashina for critical reading of the manuscript and Henry Escobar and Tim Conrad of MSSM UNIX cluster support group for server administration.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts032">doi:10.1093/bioinformatics/bts032</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22257670">pmid:22257670</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3289923/">pmcid:PMC3289923</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/sna7upcwrjcenjhy7v7ru7xdfy">fatcat:sna7upcwrjcenjhy7v7ru7xdfy</a> </span>
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AnsNGS: An Annotation System to Sequence Variations of Next Generation Sequencing Data for Disease-Related Phenotypes

Young-Ji Na, Yonglae Cho, Ju Han Kim
<span title="">2013</span> <i title="The Korean Society of Medical Informatics (KAMJE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/m4gmyyuhsjbq3djtjwubvabf6m" style="color: black;">Healthcare Informatics Research</a> </i> &nbsp;
AnsNGS (annotation system of sequence variations for next generation sequencing data) is a new tool for annotating detected variants using disease-associated variants. II.  ...  www.e-hir.orgAnsNGS: An Annotation System for Next Generation Sequencing Data  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4258/hir.2013.19.1.50">doi:10.4258/hir.2013.19.1.50</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23626918">pmid:23626918</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3633172/">pmcid:PMC3633172</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lcpo3iptx5hetmojftlmgq76h4">fatcat:lcpo3iptx5hetmojftlmgq76h4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829034453/http://www.snubi.org/~juhan/pubFiles/Hir019-01-08.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/62/00/620081787927ab3cf72558e4f7ee86a3e5d3c313.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4258/hir.2013.19.1.50"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3633172" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

In-depth annotation of SNPs arising from resequencing projects using NGS-SNP

J. R. Grant, A. S. Arantes, X. Liao, P. Stothard
<span title="2011-06-22">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Included among the annotations, several of which are not available from any existing SNP annotation tools, are the results of detailed comparisons with orthologous sequences.  ...  NGS-SNP is a collection of command-line scripts for providing rich annotations for SNPs identified by the sequencing of whole genomes from any organism with reference sequences in Ensembl.  ...  Apart from NGS-SNP we are aware of two tools designed to annotate the very large SNP lists generated by whole-genome resequencing of humans and nonhuman species.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btr372">doi:10.1093/bioinformatics/btr372</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21697123">pmid:21697123</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3150039/">pmcid:PMC3150039</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gcemkzvgmbg3bjilae2h72zl7u">fatcat:gcemkzvgmbg3bjilae2h72zl7u</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3150039/PMC3150039-btr372.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6b/be/6bbe1664d0eb784590ef7658bdbbbaf53fa45d72.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btr372"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3150039" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Review of Bioinformatics Model and Computational Software of Next Generation Sequencing

Jalilah Arijah Mohd Kamarudin, Afnizanfaizal Abdullah, Roselina Sallehuddin
<span title="2019-05-31">2019</span> <i title="Penerbit UTM Press"> International Journal of Innovative Computing </i> &nbsp;
This review paper gives an overview of the computational software and bioinformatics model that has been used for next generation sequencing.  ...  In the past decade it has become increasingly the effort for researcher to surpass the bioinformatics challenges foremost in next generation sequencing (NGS).  ...  TABLE 1 . 1 Summary of Bioinformatics Model and Computational Software for Next Generation Sequencing VarScan Tool for variant detection of short reads alignments Open source http://genome.wustl.edu/tools  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.11113/ijic.v9n1.217">doi:10.11113/ijic.v9n1.217</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hi3g4qblefgu3ae4vmtjyml6ym">fatcat:hi3g4qblefgu3ae4vmtjyml6ym</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200307032927/https://ijic.utm.my/index.php/ijic/article/download/217/138" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/31/d1/31d10daec862510ee437fec6eb7911b52db17ceb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.11113/ijic.v9n1.217"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

EagleView: A genome assembly viewer for next-generation sequencing technologies

W. Huang, G. Marth
<span title="2008-07-30">2008</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nwro4atxwbec5pfkpfslaxbdae" style="color: black;">Genome Research</a> </i> &nbsp;
EagleView has been used in our own lab and by over 100 research labs worldwide for next-generation sequence analyses. The EagleView software is freely available for not-for-profit use at  ...  The emergence of high-throughput next-generation sequencing technologies (e.g., 454 Life Sciences [Roche], Illumina sequencing [formerly Solexa sequencing]) has dramatically sped up whole-genome de novo  ...  R01 HG003698) from the National Human Genome Research Institute, National Institutes of Health.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.076067.108">doi:10.1101/gr.076067.108</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18550804">pmid:18550804</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2527701/">pmcid:PMC2527701</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/h3lt2oinebed7fplvt3uvm7wpu">fatcat:h3lt2oinebed7fplvt3uvm7wpu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190304044740/http://pdfs.semanticscholar.org/c106/cb3d0d1b163009a4dcc97102b76b9485a84e.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c1/06/c106cb3d0d1b163009a4dcc97102b76b9485a84e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.076067.108"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2527701" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genomics software: The view from 10,000 feet

Michael E Weale
<span title="2009-10-01">2009</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/oqcgtjrrffbixmejmuqswbwhd4" style="color: black;">Human Genomics</a> </i> &nbsp;
The rate of change in genomics, and 'omics generally, shows no signs of slowing down. Related analysis software is struggling to keep apace. This paper provides a brief review of the field.  ...  problem, but one of general interest due to the role of the immune response system in many diseases, is to call classical human leukocyte antigen (HLA) genotypes from SNPs typed in the HLA region of chromosome  ...  Analytical tools for dealing with molecular data have always lagged behind the acceleration of highthroughput methods for generating them, and that seems especially true at the present time.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1479-7364-4-1-56">doi:10.1186/1479-7364-4-1-56</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mpbapejj55ex7dvwvjkezbl72q">fatcat:mpbapejj55ex7dvwvjkezbl72q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191212013823/https://humgenomics.biomedcentral.com/track/pdf/10.1186/1479-7364-4-1-56" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c4/0c/c40c7aaece3935e2094c77781ea00c1e169be6e2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1479-7364-4-1-56"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

Genomics software: The view from 10,000 feet

Michael E Weale
<span title="">2009</span> <i title="Springer (Biomed Central Ltd.)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/oqcgtjrrffbixmejmuqswbwhd4" style="color: black;">Human Genomics</a> </i> &nbsp;
The rate of change in genomics, and 'omics generally, shows no signs of slowing down. Related analysis software is struggling to keep apace. This paper provides a brief review of the field.  ...  problem, but one of general interest due to the role of the immune response system in many diseases, is to call classical human leukocyte antigen (HLA) genotypes from SNPs typed in the HLA region of chromosome  ...  Analytical tools for dealing with molecular data have always lagged behind the acceleration of highthroughput methods for generating them, and that seems especially true at the present time.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19951894">pmid:19951894</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3500188/">pmcid:PMC3500188</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uq3wiu6minbwznziwnphksfwg4">fatcat:uq3wiu6minbwznziwnphksfwg4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210180854/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3500188&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/7d/e9/7de912e0032f10f0c083499917ab4b850fe9291c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3500188" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Exome-assistant: a rapid and easy detection of disease-related genes and genetic variations from exome sequencing

Qi Liu, Enjian Shen, Qingjie Min, Xueying Li, Xin Wang, Xianfeng Li, Zhong Sheng Sun, Jinyu Wu
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
Results: In this study, Exome-assistant (http://122.228.158.106/exomeassistant), a convenient tool for submitting and annotating single nucleotide polymorphisms (SNPs) and insertion/deletion variations  ...  Protein-coding regions in human genes harbor 85% of the mutations that are associated with disease-related traits.  ...  Acknowledgements This study was supported by the National Natural Science Foundation of China (Grant No. 31100917  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-13-692">doi:10.1186/1471-2164-13-692</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23231371">pmid:23231371</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3539923/">pmcid:PMC3539923</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nzbfmm3csrgf5g7p6ca2hzfjtq">fatcat:nzbfmm3csrgf5g7p6ca2hzfjtq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830131545/https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-13-692?site=http://bmcgenomics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0b/49/0b49964bd3c3ef31c1be4c7e0b6223c443f82103.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-13-692"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3539923" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

GenomeGems: evaluation of genetic variability from deep sequencing data

Sharon Ben-Zvi, Adi Givati, Noam Shomron
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/gl3hmlq4ebd3jcx3yuj2yfzivq" style="color: black;">BMC Research Notes</a> </i> &nbsp;
The tool allows the user to compare and visualize SNPs from multiple experiments and to easily load SNP data onto the UCSC Genome browser for further detailed information.  ...  Figure 12 The Additional Information interface enables quick transfer to suggested additional databases for further analysis of SNPs.  ...  Additional Information-suggests additional external links for further investigation and annotation of specific SNPs and of the impact of amino acid changes on human proteins.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1756-0500-5-338">doi:10.1186/1756-0500-5-338</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22748151">pmid:22748151</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3499170/">pmcid:PMC3499170</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bedz7il7krg6ffsufgtzlwytfe">fatcat:bedz7il7krg6ffsufgtzlwytfe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170819145022/https://bmcresnotes.biomedcentral.com/track/pdf/10.1186/1756-0500-5-338?site=bmcresnotes.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/e8/f8/e8f81e885fadd71e0676096f499fc85f6748649a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1756-0500-5-338"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3499170" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

SNPAAMapper: An efficient genome-wide SNP variant analysis pipeline for next-generation sequencing data
English

Yongsheng Bai, James Cavalcoli
<span title="2013-10-16">2013</span> <i title="Biomedical Informatics"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iztfdaqh6bclfpgb2mitxtn5sm" style="color: black;">Bioinformation</a> </i> &nbsp;
However, publicly available tools dealing with the downstream analysis of genome-wide variants are fewer and have limited functionality.  ...  Many NGS analysis tools focusing on read alignment and variant calling functions for exome sequencing data have been developed in recent years.  ...  Funding: This pipeline development was supported in part by funds from the Medical School at the University of Michigan.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6026/97320630009870">doi:10.6026/97320630009870</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24250114">pmid:24250114</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3819573/">pmcid:PMC3819573</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/raqnyosptvfh3hdgkqd2z67zt4">fatcat:raqnyosptvfh3hdgkqd2z67zt4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190429080357/http://www.bioinformation.net/009/97320630009870.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3a/87/3a87457ffd0c30c024434b18cb2ee0fcf2659e01.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6026/97320630009870"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3819573" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Next-generation gene catalogues and genomics tools focused on forestry research

Philippe Rigault
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/noie53zo7fdytpet5j552fhwny" style="color: black;">BMC Proceedings</a> </i> &nbsp;
artifact-free annotated sequences desirable for the production of quality tools for genomics research.  ...  Next-generation sequencing technologies have revolutionized the field of genomics and have reached the capacity to generate enough quality data to sequence and assemble thousands of genomes and gene catalogues  ...  artifact-free annotated sequences desirable for the production of quality tools for genomics research.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1753-6561-5-s7-p174">doi:10.1186/1753-6561-5-s7-p174</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3240024/">pmcid:PMC3240024</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pu2vf3mmmfaeppfwb3pi36owmu">fatcat:pu2vf3mmmfaeppfwb3pi36owmu</a> </span>
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BALL-SNP: combining genetic and structural information to identify candidate non-synonymous single nucleotide polymorphisms

Sabine C. Mueller, Christina Backes, Olga V. Kalinina, Benjamin Meder, Daniel Stöckel, Hans-Peter Lenhof, Eckart Meese, Andreas Keller
<span title="2015-07-01">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/odidfbcgarekjpyyfxpdptajxa" style="color: black;">Genome Medicine</a> </i> &nbsp;
Next-Generation Sequencing (NGS) data analysis however still remains a great challenge.  ...  The modular and flexible implementation allows for straightforward integration of different databases for pathogenic and benign variants, but also enables the integration of pathogenicity prediction tools  ...  The increasing adoption of Next-Generation Sequencing (NGS) in clinical applications leads to a substantial amount of novel nsSNPs.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13073-015-0190-y">doi:10.1186/s13073-015-0190-y</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26191084">pmid:26191084</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4506604/">pmcid:PMC4506604</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pqk3xmr6qfcjbe2li6umkkin4y">fatcat:pqk3xmr6qfcjbe2li6umkkin4y</a> </span>
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