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Protocols

SoyKB specifications

Information


Unique identifier OMICS_03297
Name SoyKB
Alternative name Soybean Knowledge Base
Restrictions to use None
Maintained Yes

Taxon


  • Plants and Fungi
    • Glycine max

Maintainer


  • person_outline Trupti Joshi

Publications for Soybean Knowledge Base

SoyKB citations

 (10)
call_split

Drought Stress Causes a Reduction in the Biosynthesis of Ascorbic Acid in Soybean Plants

2017
Front Plant Sci
PMCID: 5471321
PMID: 28663755
DOI: 10.3389/fpls.2017.01042
call_split See protocol

[…] At3g02870.1), GalDH (L-galactose dehydrogenase, At4g33670.1), GalLDH (At3g47930.1) and VTC3 (a protein kinase, AT2G40860.1). Search was carried out against the corresponding protein sequences of the Soybean Knowledge Base genome (version Wm82.a1.v1.1) () and the Medicago truncatula genome (version 4.0).The predicted amino acid sequences for each step in the pathway were aligned using MAFFT using […]

call_split

PGen: large scale genomic variations analysis workflow and browser in SoyKB

2016
BMC Bioinformatics
PMCID: 5074001
PMID: 27766951
DOI: 10.1186/s12859-016-1227-y
call_split See protocol

[…] n also be applied by modifying the configuration file of a PGen workflow. Outputs are generated as BAM and VCF standard formats that are accessible through both the iPlant data store (iDS) [] and the SoyKB database via the newly built NGS resequencing data browser. The BAM and VCF results files are further utilized for downstream analyses of SNP annotations, CNVs, and genotype-phenotype relationsh […]

library_books

Soybean Roots Grown under Heat Stress Show Global Changes in Their Transcriptional and Proteomic Profiles

2016
Front Plant Sci
PMCID: 4843095
PMID: 27200004
DOI: 10.3389/fpls.2016.00517

[…] t one read in both biological replicates (Table ). The RNAseq gene expression, proteomic expression, and differential expression datasets are all available for browsing in the Soybean Knowledge Base (SoyKB; http://www.soykb.org/; Joshi et al., , ). […]

library_books

Evaluation of genetic variation among Brazilian soybean cultivars through genome resequencing

2016
BMC Genomics
PMCID: 4752768
PMID: 26872939
DOI: 10.1186/s12864-016-2431-x

[…] r SNP/InDel calling of the genome. In both cases, we used the HaplotypeCaller module of GATK.The analysis was conducted using the bioinformatic NGS resequencing data analysis workflow [] developed in SoyKB for SNP and Indel calling. XSEDE [] was used as the computing infrastructure, iPlant as the data and cloud infrastructure [], and the Pegasus workflow systems [] to control and coordinate the da […]

library_books

Genome wide transcriptome analysis of soybean primary root under varying water deficit conditions

2016
BMC Genomics
PMCID: 4714440
PMID: 26769043
DOI: 10.1186/s12864-016-2378-y

[…] 2 ratio > 2 as the threshold to judge the significance of gene expression differences. The analyzed RNA-Seq gene expressions and the differential gene expression results are available for browsing in Soybean Knowledge Base (SoyKB) [] at http://soykb.org. The datasets (SoyKB/Information/Dataset 17) can be browsed using the differential expression analysis suite tools, which provide access to the ge […]

library_books

Using RNA Seq Data to Evaluate Reference Genes Suitable for Gene Expression Studies in Soybean

2015
PLoS One
PMCID: 4562714
PMID: 26348924
DOI: 10.1371/journal.pone.0136343

[…] o the genome Glycine max 275 v2.0. The alignment statistics were shown in .Two additional RNA-Seq datasets were obtained from public databases. One of the datasets published in 2010 was obtained from SoyKB [, ]. The sequencing libraries—young leaf, seed (14–17 DAF), seed (10–13 DAF), seed (21 DAF), one cm pod, pod-shell (14–17 DAF), pod-shell (10–13 DAF), nodule, root, seed (25 DAF), seed (28 DAF) […]

Citations

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SoyKB institution(s)
Department of Computer Science, University of Missouri, Columbia, MO, USA; Christopher S. Bond Life Sciences Center, University of Missouri, Columbia, MO, USA; National Center for Soybean Biotechnology, University of Missouri, Columbia, MO, USA; Informatics Institute, University of Missouri, Columbia, MO, USA; Division of Plant Sciences, University of Missouri, Columbia, MO, USA

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