Soybean database statistics

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Protocols

Soybean database specifications

Information


Unique identifier OMICS_27402
Name Soybean database
Restrictions to use None
Database management system MySQL
Community driven No
Data access File download, Browse
User data submission Not allowed
Maintained Yes

Maintainer


  • person_outline EUCANEXT team

Publication for Soybean database

Soybean database citations

 (16)
library_books

Analysis of EF Hand Proteins in Soybean Genome Suggests Their Potential Roles in Environmental and Nutritional Stress Signaling

2017
Front Plant Sci
PMCID: 5443154
PMID: 28596783
DOI: 10.3389/fpls.2017.00877

[…] n EF-hand domain or in the family of Ca2+-binding proteins which included domains PF00036, PTHR10891, PS00018, PS50222, SM00054, and SSF47473, were collected by keyword searching from the Phytozome’s soybean database. Furthermore, “EF-hand,” “calmodulin,” “calmodulin-like,” “calcineurin B-like,” and “calcium-dependent protein kinase” were each used as a key word to perform homolog searches. In add […]

library_books

A Transcriptomic Comparison of Two Bambara Groundnut Landraces under Dehydration Stress

2017
Genes
PMCID: 5406868
PMID: 28420201
DOI: 10.3390/genes8040121

[…] ere designed using Primer-BLAST [] for the chosen genes. The primers were designed in three steps. Firstly, the target gene sequence to which the primers needed to be designed was downloaded from the soybean database. Secondly, the soybean-specific target gene sequence was blasted against a bambara groundnut transcriptome generated from RNA-sequencing data for a low-temperature stress experiment [ […]

call_split

Whole genome wide transcript profiling to identify differentially expressed genes associated with seed field emergence in two soybean low phytate mutants

2017
BMC Plant Biol
PMCID: 5242038
PMID: 28100173
DOI: 10.1186/s12870-016-0953-7
call_split See protocol

[…] ing unknown nucleotides “Ns”), reads of copy number = 1 and reads of lengths less than 20 bp, yielding a dataset consisting of clean reads. For the annotation of reads, clean reads were mapped to the soybean database using software TopHat []. Mismatches of no more than two bases were allowed in the alignment. The number of clean reads for each gene was calculated and normalized using a variation o […]

library_books

Molecular Characterization of Soybean Pterocarpan 2 Dimethylallyltransferase in Glyceollin Biosynthesis: Local Gene and Whole Genome Duplications of Prenyltransferase Genes Led to the Structural Diversity of Soybean Prenylated Isoflavonoids

2016
PMCID: 5159607
PMID: 27986914
DOI: 10.1093/pcp/pcw178

[…] Putative genes encoding isoflavonoid PTs were retrieved from the soybean database at Phytozome v11.0 (https://phytozome.jgi.doe.gov/pz/portal.html#) using the amino acid sequence of A. thaliana HPT (AtVTE2‐1, AY089963) as the query, and corresponding transcripts we […]

library_books

Identification and functional characterization of the sulfate transporter gene GmSULTR1;2b in soybean

2016
BMC Genomics
PMCID: 4874011
PMID: 27206527
DOI: 10.1186/s12864-016-2705-3

[…] Twelve Arabidopsis SULTRs were used as query sequences for BLASTN searches of the soybean database in Phytozome (http://www.phytozome.net) with default parameters; redundant sequences were manually discarded. Twenty-eight putative SULTR genes, located on 15 chromosomes, were identi […]

library_books

Comparative Proteomic Analysis of Soybean Leaves and Roots by iTRAQ Provides Insights into Response Mechanisms to Short Term Salt Stress

2016
Front Plant Sci
PMCID: 4850148
PMID: 27200046
DOI: 10.3389/fpls.2016.00573

[…] The raw MS/MS data files acquired from the Orbitrap were processed by a thorough database searching considering biological modification and amino acid substitution against the Uniprot Soybean database with 71,042 entries (downloaded on May 16, 2013), using Proteome Discoverer 1.4 (Thermo Scientific Inc., Bremen, Germany) with the SEQUEST algorithm. The following parameters were use […]

Citations

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Soybean database institution(s)
Laboratório de Genômica e Expressão, Departamento de Genética, Evolução e Bioagentes, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, Brazil; Empresa Brasileira de Pesquisa Agropecuária, Londrina, Brazil; Centro Nacional de Processamento de Alto Desempenho em São Paulo, Universidade Estadual de Campinas, Campinas, Brazil
Soybean database funding source(s)
Supported by CNPQ (Conselho Nacional de Desenvolvimento Científico e Tecnológico- Brazil).

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