title: Rice SNP-seek database update: new SNPs, indels, and queries.
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. 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.
authors.affiliation: International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.
authors.forename: Locedie
authors.initials: L
authors.lastname: Mansueto
authors.affiliation: International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.
authors.forename: Roven Rommel
authors.initials: RR
authors.lastname: Fuentes
authors.affiliation: International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.
authors.forename: Frances Nikki
authors.initials: FN
authors.lastname: Borja
authors.affiliation: International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.
authors.forename: Jeffery
authors.initials: J
authors.lastname: Detras
authors.affiliation: International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.
authors.forename: Juan Miguel
authors.initials: JM
authors.lastname: Abriol-Santos
authors.affiliation: International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.
authors.forename: Dmytro
authors.initials: D
authors.lastname: Chebotarov
authors.affiliation: International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.
authors.forename: Millicent
authors.initials: M
authors.lastname: Sanciangco
authors.affiliation: International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.|Boyce Thompson Institute, Ithaca, NY 14853, USA.
authors.forename: Kevin
authors.initials: K
authors.lastname: Palis
authors.affiliation: Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85750, USA.
authors.forename: Dario
authors.initials: D
authors.lastname: Copetti
authors.affiliation: Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.|DOE Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Poliakov
authors.affiliation: Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.|DOE Joint Genome Institute, Walnut Creek, CA 94598, USA.
authors.forename: Inna
authors.initials: I
authors.lastname: Dubchak
authors.affiliation: Softberry, Inc., Mount Kisco, NY 10549, USA.
authors.forename: Victor
authors.initials: V
authors.lastname: Solovyev
authors.affiliation: International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.|Arizona Genomics Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85750, USA.
authors.forename: Rod A
authors.initials: RA
authors.lastname: Wing
authors.affiliation: International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.
authors.forename: Ruaraidh Sackville
authors.initials: RS
authors.lastname: Hamilton
authors.affiliation: International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.
authors.forename: Ramil
authors.initials: R
authors.lastname: Mauleon
authors.affiliation: International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines.
authors.forename: Kenneth L
authors.initials: KL
authors.lastname: McNally
authors.affiliation: International Rice Research Institute, College, Los Baños, Laguna 4031, Philippines n.alexandrov@irri.org.
authors.forename: Nickolai
authors.initials: N
authors.lastname: Alexandrov
mesh_terms: D000483:Alleles; D019295:Computational Biology / Q000379:methods; D030561:Databases, Nucleic Acid; D005787:Gene Frequency; D056426:Genetic Loci; D018745:Genome, Plant; D023281:Genomics / Q000379:methods; D005838:Genotype; D054643:INDEL Mutation; D012275:Oryza / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D057386:Search Engine; D012984:Software; D014584:User-Computer Interface; D064878:Web Browser