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Published (Version of record)CC BY V4.0, Open Access
Published (Version of record)CC BY V4.0, Open
Journal article
Rice SNP-seek database update: new SNPs, indels, and queries
Nucleic acids Research, Vol.45(Database issue), pp.D1075-D1081
29/11/2016
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Abstract
We describe updates to the Rice SNP-Seek Database since its first release. We ran a new SNP-calling pipeline followed by filtering that resulted in complete, base, filtered and core SNP datasets. Besides the Nipponbare reference genome, the pipeline was run on genome assemblies of IR 64, 93-11, DJ 123 and Kasalath. New genotype query and display features are added for reference assemblies, SNP datasets and indels. JBrowse now displays BAM, VCF and other annotation tracks, the additional genome assemblies and an embedded VISTA genome comparison viewer. Middleware is redesigned for improved performance by using a hybrid of HDF5 and RDMS for genotype storage. Query modules for genotypes, varieties and genes are improved to handle various constraints. An integrated list manager allows the user to pass query parameters for further analysis. The SNP Annotator adds traits, ontology terms, effects and interactions to markers in a list. Webservice calls were implemented to access most data. These features enable seamless querying of SNPSeek across various biological entities, a step toward semi-automated gene-trait association discovery. URL: http://snp-seek.irri.org.
Details
- Title
- Rice SNP-seek database update: new SNPs, indels, and queries
- Creators
- Locedie Mansueto - Southern Cross University, Faculty of Science and EngineeringRoven Rommel Fuentes - International Rice Research InstituteFrances Nikki Borja - International Rice Research Institute (Phillipines)Jeffery Detras - International Rice Research Inst., Los Banos (Philippines)Juan Miguel Abriol-Santos - International Rice Research Inst., Los Banos (Philippines)Dmytro Chebotarov - International Rice Research InstituteMillicent Sanciangco - International Rice Research InstituteKevin Palis - International Rice Research InstituteDario Copetti - University of ArizonaAlexandre Poliakov - Joint Genome InstituteInna Dubchak - Joint Genome InstituteVictor Solovyev - Softberry, Inc., Mount Kisco, NY (United States)Rod A Wing - International Rice Research InstituteRuaraidh Sackville Hamilton - International Rice Research Institute (Phillipines)Ramil Mauleon - International Rice Research InstituteKenneth L McNally - International Rice Research InstituteNickolai Alexandrov - International Rice Research InstituteLawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
- Publication Details
- Nucleic acids Research, Vol.45(Database issue), pp.D1075-D1081
- Publisher
- Oxford University Press
- Identifiers
- 991012978826702368
- Copyright
- The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial reuse, please contactjournals.permissions@oup.com
- Academic Unit
- Faculty of Science and Engineering; Science
- Language
- English
- Resource Type
- Journal article