Rice SNP-seek database update: new SNPs, indels, and queries
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 1...
| Main Authors: | , , , , , , , , , , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Oxford University Press
2017
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| Online Access: | https://hdl.handle.net/10568/165174 |
| _version_ | 1855536910163771392 |
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| author | Mansueto, Locedie Fuentes, Roven Rommel Borja, Frances Nikki Detras, Jeffery Abriol-Santos, Juan Miguel Chebotarov, Dmytro Sanciangco, Millicent Palis, Kevin Copetti, Dario Poliakov, Alexandre Dubchak, Inna Solovyev, Victor Wing, Rod A. Hamilton, Ruaraidh Sackville Mauleon, Ramil McNally, Kenneth L. Alexandrov, Nickolai |
| author_browse | Abriol-Santos, Juan Miguel Alexandrov, Nickolai Borja, Frances Nikki Chebotarov, Dmytro Copetti, Dario Detras, Jeffery Dubchak, Inna Fuentes, Roven Rommel Hamilton, Ruaraidh Sackville Mansueto, Locedie Mauleon, Ramil McNally, Kenneth L. Palis, Kevin Poliakov, Alexandre Sanciangco, Millicent Solovyev, Victor Wing, Rod A. |
| author_facet | Mansueto, Locedie Fuentes, Roven Rommel Borja, Frances Nikki Detras, Jeffery Abriol-Santos, Juan Miguel Chebotarov, Dmytro Sanciangco, Millicent Palis, Kevin Copetti, Dario Poliakov, Alexandre Dubchak, Inna Solovyev, Victor Wing, Rod A. Hamilton, Ruaraidh Sackville Mauleon, Ramil McNally, Kenneth L. Alexandrov, Nickolai |
| author_sort | Mansueto, Locedie |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | 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. Web-service calls were implemented to access most data. These features enable seamless querying of SNP-Seek across various biological entities, a step toward semi-automated gene-trait association discovery. URL: http://snp-seek.irri.org |
| format | Journal Article |
| id | CGSpace165174 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace1651742024-12-19T14:13:24Z Rice SNP-seek database update: new SNPs, indels, and queries Mansueto, Locedie Fuentes, Roven Rommel Borja, Frances Nikki Detras, Jeffery Abriol-Santos, Juan Miguel Chebotarov, Dmytro Sanciangco, Millicent Palis, Kevin Copetti, Dario Poliakov, Alexandre Dubchak, Inna Solovyev, Victor Wing, Rod A. Hamilton, Ruaraidh Sackville Mauleon, Ramil McNally, Kenneth L. Alexandrov, Nickolai 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. Web-service calls were implemented to access most data. These features enable seamless querying of SNP-Seek across various biological entities, a step toward semi-automated gene-trait association discovery. URL: http://snp-seek.irri.org 2017-01-04 2024-12-19T12:54:46Z 2024-12-19T12:54:46Z Journal Article https://hdl.handle.net/10568/165174 en Open Access Oxford University Press Mansueto, Locedie; Fuentes, Roven Rommel; Borja, Frances Nikki; Detras, Jeffery; Abriol-Santos, Juan Miguel; Chebotarov, Dmytro; Sanciangco, Millicent; Palis, Kevin; Copetti, Dario; Poliakov, Alexandre; Dubchak, Inna; Solovyev, Victor; Wing, Rod A.; Hamilton, Ruaraidh Sackville; Mauleon, Ramil; McNally, Kenneth L. and Alexandrov, Nickolai. 2017. Rice SNP-seek database update: new SNPs, indels, and queries. Nucleic Acids Res, Volume 45 no. D1 p. D1075-D1081 |
| spellingShingle | Mansueto, Locedie Fuentes, Roven Rommel Borja, Frances Nikki Detras, Jeffery Abriol-Santos, Juan Miguel Chebotarov, Dmytro Sanciangco, Millicent Palis, Kevin Copetti, Dario Poliakov, Alexandre Dubchak, Inna Solovyev, Victor Wing, Rod A. Hamilton, Ruaraidh Sackville Mauleon, Ramil McNally, Kenneth L. Alexandrov, Nickolai Rice SNP-seek database update: new SNPs, indels, and queries |
| title | Rice SNP-seek database update: new SNPs, indels, and queries |
| title_full | Rice SNP-seek database update: new SNPs, indels, and queries |
| title_fullStr | Rice SNP-seek database update: new SNPs, indels, and queries |
| title_full_unstemmed | Rice SNP-seek database update: new SNPs, indels, and queries |
| title_short | Rice SNP-seek database update: new SNPs, indels, and queries |
| title_sort | rice snp seek database update new snps indels and queries |
| url | https://hdl.handle.net/10568/165174 |
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