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SNiPloid: A Utility to Exploit High-Throughput SNP Data Derived from RNA-Seq in Allopolyploid Species

Marine Peralta, Marie-Christine Combes, Alberto Cenci, Philippe Lashermes, Alexis Dereeper
2013 International Journal of Plant Genomics  
High-throughput sequencing is a common approach to discover SNP variants, especially in plant species.  ...  SNiPloid can compare SNPs obtained from a sample to estimate the subgenome contribution to the transcriptome or SNPs obtained from two polyploid accessions to search for SNP divergence.  ...  Conclusions To our knowledge, SNiPloid is the first Web tool dedicated and optimized for the SNP analysis of RNA-Seq data obtained from an allopolyploid species.  ... 
doi:10.1155/2013/890123 pmid:24163691 pmcid:PMC3791807 fatcat:5mr3qpfasnh7zojinsgegmpjia

NABIC SNP: an integrated database for SNP markers

Chang-Kug Kim, So-Youn Won, Young-Joo Seol, Tae-Ho Lee
2015 Bioinformation  
in a high-throughput manner.  ...  The National Agricultural Biotechnology Information Center (NABIC) constructed a web-based database to provide information about 54,310 single nucleotide polymorphisms (SNPs) identified in the seven species  ...  Acknowledgement: This study was conducted with support from the Research Program for Agricultural Science & Technology Developmen t (Project No.  ... 
doi:10.6026/97320630011369 pmid:26339155 pmcid:PMC4546998 fatcat:6e5ed7dv3zgh5mge4ltrb5omza

In This Issue

2002 Comparative and Functional Genomics  
The paper includes a detailed discussion of the statistical considerations for the analysis of microarray data.  ...  Although some significant differences were found, none of them have as yet been shown to relate to a conceivable consequence of the mutations, or compensation for the mutations.  ...  High-throughout SNP genotyping technologies Suzanne Jenkins and Tim Gibson discuss the advantages and drawbacks of the chemistries and platforms available for high-throughput SNP genotyping.  ... 
doi:10.1002/cfg.142 fatcat:ju3l6teaafbffnm4gii7gtxcma

DDBJ Read Annotation Pipeline: A Cloud Computing-Based Pipeline for High-Throughput Analysis of Next-Generation Sequencing Data

H. Nagasaki, T. Mochizuki, Y. Kodama, S. Saruhashi, S. Morizaki, H. Sugawara, H. Ohyanagi, N. Kurata, K. Okubo, T. Takagi, E. Kaminuma, Y. Nakamura
2013 DNA Research  
Users may smoothly switch between the two components in the pipeline, facilitating web-based operations on a supercomputer for high-throughput data analysis.  ...  The DNA Data Bank of Japan (DDBJ) of the National Institute of Genetics (NIG) has initiated a cloud computing-based analytical pipeline, the DDBJ Read Annotation Pipeline (DDBJ Pipeline), for a high-throughput  ...  Acknowledgements: We thank Yasuhiro Tanizawa, Natsuko Sakakura, Shigeki Watanabe, and Naoko Sakamoto for the support of pipeline users. We particularly thank Toshihisa Okido for helpful discussions.  ... 
doi:10.1093/dnares/dst017 pmid:23657089 pmcid:PMC3738164 fatcat:ayzq4fhuvvdwpoqw7qjsre25ii

SNP HiTLink: a high-throughput linkage analysis system employing dense SNP data

Yoko Fukuda, Yasuo Nakahara, Hidetoshi Date, Yuji Takahashi, Jun Goto, Akinori Miyashita, Ryozo Kuwano, Hiroki Adachi, Eiji Nakamura, Shoji Tsuji
2009 BMC Bioinformatics  
Results: We have developed SNP HiTLink (SNP High Throughput Linkage analysis system).  ...  step, thus, necessitating a high-throughput platform.  ...  Medical Science, and Scientific Research (A) from the Ministry of Education, Culture, Sports, Science and Technology of Japan.  ... 
doi:10.1186/1471-2105-10-121 pmid:19393044 pmcid:PMC2680848 fatcat:l4fubz27pbhmdi56c74utuokiy

SCAN: SNP and copy number annotation

Eric R. Gamazon, Wei Zhang, Anuar Konkashbaev, Shiwei Duan, Emily O. Kistner, Dan L. Nicolae, M. Eileen Dolan, Nancy J. Cox
2009 Computer applications in the biosciences : CABIOS  
For each gene, SCAN provides annotations on: (i) eQTLs for the gene (both local and distant SNPs) and (ii) the coverage of all variants in the HapMap at that gene on each high-throughput platform.  ...  the variant and how well the SNP is covered by different high-throughput platforms; (iii) summary information available from public databases (e.g. physical and functional annotations); and (iv) summary  ...  ACKNOWLEDGEMENTS The authors are grateful to members from the Dolan Lab and from the Cox Lab for testing the database and providing helpful feedback.  ... 
doi:10.1093/bioinformatics/btp644 pmid:19933162 pmcid:PMC2852202 fatcat:zv2uvdfzszfstg3tnbpculopla

BnaGVD: A genomic variation database of rapeseed (Brassica napus)

Tao Yan, Yao Yao, Dezhi Wu, Lixi Jiang
2021 Plant and Cell Physiology  
Extensive tools for practical purposes should be developed to efficiently utilize these large raw data.  ...  With the rapid progress on high-throughput sequencing technologies and the reduction of sequencing cost, large-scale genomic data of a specific crop have become available.  ...  With 34,591,899 SNPs, 12,281,923 InDels and their corresponding gene annotations, a web interface was designed to search for, browse, analyze, and download data.  ... 
doi:10.1093/pcp/pcaa169 pmid:33399824 fatcat:ydbwn2zto5edrppyu23jpgmame

BnaSNPDB: An interactive web portal for the efficient retrieval and analysis of SNPs among 1,007 rapeseed accessions

Tao Yan, Qian Wang, Antony Maodzeka, Dezhi Wu, Lixi Jiang
2020 Computational and Structural Biotechnology Journal  
Here, we present BnaSNPDB, an interactive web portal with a user-friendly interface that provides multiple analysis modules for retrieving, analyzing, and visualizing single nucleotide polymorphisms among  ...  The rapid development of high-throughput sequencing technology and the decrease in sequencing costs provide valuable resources and great opportunities for researchers to investigate genomic variations  ...  The Phylogenetic function is designed to perform phylogenetic analysis and explore the genetic distances and evolutionary history based on high-density SNP data (Fig. 4A) .  ... 
doi:10.1016/j.csbj.2020.09.031 pmid:33101613 pmcid:PMC7558807 fatcat:u3eho6cacrffpjgdk2yrz4vn2u

Varietas: a functional variation database portal

J. Paananen, R. Ciszek, G. Wong
2010 Database: The Journal of Biological Databases and Curation  
Current high-throughput technologies for investigating genomic variation in large population based samples produce data on a scale of millions of variations.  ...  In order to help researchers locate the most promising associations, we have developed a web-based database portal called Varietas.  ...  Acknowledgements The authors would like to thank Mitja Kurki and Petri Pehkonen for helpful comments during the design and implementation of this work. Conflict of interest. None declared.  ... 
doi:10.1093/database/baq016 pmid:20671203 pmcid:PMC2997604 fatcat:o3rfrhjibzf2lm2yg65xrug5ny

Gene-Based Marker Systems in Plants: High Throughput Approaches for Marker Discovery and Genotyping [chapter]

Rajeev K Varshney
2009 Molecular Techniques in Crop Improvement  
For instance, high-throughput and low cost genotyping assays for gene-based markers offers the possibility to accelerate the trait mapping based on high-density linkage mapping as well as genome-scanning  ...  The availability of inexpensive high-density SNP-genotyping arrays is encouraging the plant genetics and breeding community to undertake genome-wide marker genotyping for a variety of applications.  ...  A web-based cyber infrastructure platform, called Alpheus (, is very useful for pipelining, visualization and analysis of GigaBase-scale sequence data for identification of SNPs  ... 
doi:10.1007/978-90-481-2967-6_5 fatcat:haumrsfub5erlagnk3jczz362q

An Overview on the Main Technical Processes of Restriction-Site Associated DNA Sequencing (RAD-Seq)

Qingqing Li, Momo Li, Jiefei Qiu, Fenfen Chen, Min Chen, Qilin Wang, Guangyu Li, Aiwei Guo
2021 DEStech Transactions on Materials Science and Engineering  
As sequencing costs have dropped, RAD-Seq has moved from being primarily a SNP discovery tool to being a method for high-throughput genotyping of populations.  ...  Restriction site-associated DNA sequencing (RAD-seq) is a critical enabling genotyping method based on whole-genome restriction sites developed on the basis of second-generation sequencing and nowadays  ...  As sequencing costs have dropped, RAD-Seq has moved from being primarily a SNP discovery tool to being a method for high-throughput genotyping of populations [6] .  ... 
doi:10.12783/dtmse/ameme2020/35548 fatcat:cbjb3cikjjc3hhsqkrau3hofxy

Memory mapped parallel BAM file access API for high throughput sequence analysis informatics [article]

Timothy A. Pitman, Xiaomeng Huang, Gabor T. Marth, Yi Qiao
2021 bioRxiv   pre-print
Open source and freely available, we envision that mmbam will enable a new generation of high-performance informatics tools for precision medicine.  ...  We developed mmbam, a library to allow sequence analysis informatics software to access raw sequencing data stored in BAM files extremely fast.  ...  ., and Y.Q. are supported by NIH Grant U24CA209999, and an internal grant from the Center for Genomic Medicine for the development of computational pipelines supporting precision oncology.  ... 
doi:10.1101/2021.10.05.463280 fatcat:3l5476u65va2rjrxzkoxxl3wma

Current bioinformatics tools in genomic biomedical research (Review)

Andreas Teufel, Markus Krupp, Arndt Weinmann, Peter Galle
2006 International Journal of Molecular Medicine  
widening, making new approaches of high-throughput genomic analysis necessary.  ...  On the advent of a completely assembled human genome, modern biology and molecular medicine stepped into an era of increasingly rich sequence database information and high-throughput genomic analysis.  ...  Once a gene's GO characteristics are recorded, the ontology is thereby optimized for computational high-throughput analysis, allowing a highly time-saving comparison of a large amount of functional data  ... 
doi:10.3892/ijmm.17.6.967 fatcat:itvjclrd6ff6jlqaimstb45f6e

Constructing a Genome-Wide LD Map of WildA. gambiaeUsing Next-Generation Sequencing

Xiaohong Wang, Yaw A. Afrane, Guiyun Yan, Jun Li
2015 BioMed Research International  
Nearly one million SNPs that were genotyped correctly in all individual mosquitoes with 99.6% confidence were extracted from these high-throughput sequencing data.  ...  Based on these SNP genotypes, we constructed a genome-wide LD map for wildA. gambiaefrom malaria-endemic areas in Kenya and made it available through a public Website.  ...  Noah Butler from University of Oklahoma Health Sciences Center for reading the whole paper and providing insights and comments.  ... 
doi:10.1155/2015/238139 pmid:26421280 pmcid:PMC4573223 fatcat:y2k37qrayzhr5okveppvun6yey

VISTA Region Viewer (RViewer) - a computational system for prioritizing genomic intervals for biomedical studies

I. Lukashin, P. Novichkov, D. Boffelli, A. R. Paciorkowski, S. Minovitsky, S. Yang, I. Dubchak
2011 Bioinformatics  
Availability and implementation: The tool is implemented as a web application and is freely accessible on the Web at  ...  ABSTRACT Summary: Current genome browsers are designed for linear browsing of individual genomic regions, but the high-throughput nature of experiments aiming to elucidate the genetic component of human  ...  Igor Ratnere for technical support and to Tatyana Smirnova for designing the RViewer Web site.  ... 
doi:10.1093/bioinformatics/btr440 pmid:21791533 pmcid:PMC3167054 fatcat:xepyp5dxqzghzdlrzqu24cdx7i
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