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Protocols

Sinbase specifications

Information


Unique identifier OMICS_11996
Name Sinbase
Restrictions to use None
Community driven No
Data access File download, Browse
User data submission Not allowed
Version 1.0
Maintained Yes

Taxon


  • Plants and Fungi
    • Arabidopsis thaliana
    • Glycine max
    • Vitis vinifera

Maintainer


  • person_outline Xiurong Zhang

Publication for Sinbase

Sinbase citations

 (5)
library_books

Genome wide identification and expression analyses of genes involved in raffinose accumulation in sesame

2018
Sci Rep
PMCID: 5847563
PMID: 29531231
DOI: 10.1038/s41598-018-22585-2

[…] Protein sequences of genes involved in raffinose biosynthesis in Arabidopsis, such as AtGolSs and AtRSs, were used as queries to search against the protein database at Sinbase (Sesamum indicum genome database, http://ocri-genomics.org/Sinbase/index.html) by using BLASTP. Resulting sequences with an E-value of <1e−100 were analyzed manually in Pfam (http://pfam.sange […]

library_books

Phloem Conducting Cells in Haustoria of the Root Parasitic Plant Phelipanche aegyptiaca Retain Nuclei and Are Not Mature Sieve Elements

2017
PMCID: 5750636
PMID: 29206147
DOI: 10.3390/plants6040060

[…] To select P. aegyptiaca target genes, contigs of the Parasitic Plant Genome Project OrAeBC5 dataset (http://ppgp.huck.psu.edu/) were compared with the protein sequence of Sesamum indicum provided in Sinbase (http://ocri-genomics.org/Sinbase/) [] using BLASTx []. Based on the top hits, OrAeBC5_5123, OrAeBC5_14368.1, and OrAeBC5_32545.1 were chosen for PaNEN1, PaNEN4, and PaNAC45, respectively. For […]

library_books

Genome Wide Investigation of Hsf Genes in Sesame Reveals Their Segmental Duplication Expansion and Their Active Role in Drought Stress Response

2016
Front Plant Sci
PMCID: 5061811
PMID: 27790233
DOI: 10.3389/fpls.2016.01522

[…] with a gap open penalty of 10 and gap extension penalty of 0.2. The result of alignment was used for the construction of an un-rooted Maximum-Likelihood (ML) tree with a 1000 bootstrap value.Based on Sinbase information, exon-intron substructure map was constructed by the Gene Structure Display Server (GSDS 2.0), web-based bioinformatics tool (http://gsds.cbi.pku.edu.cn/) (Hu B. et al., ). Conserv […]

call_split

Identification of Sesame Genomic Variations from Genome Comparison of Landrace and Variety

2016
Front Plant Sci
PMCID: 4971434
PMID: 27536315
DOI: 10.3389/fpls.2016.01169
call_split See protocol

[…] ge was used in the calling of sequence variants (Rice et al., ). The reference genome “Zhongzhi13,” mRNA, protein sequences, repeat sequences, transposons types, and GFF file were downloaded from the Sinbase database (Wang et al., ). Transposons in “Baizhima” and “Mishuozhima” were identified by the software RepeatMasker (Version 3.3.0, http://repeatmasker.org) with the default parameters. The rep […]

library_books

Deep resequencing reveals allelic variation in Sesamum indicum

2014
BMC Plant Biol
PMCID: 4148021
PMID: 25138716
DOI: 10.1186/s12870-014-0225-3

[…] : Figure S1; Additional file : Data S1). All sequence reads were aligned against the reference genome of “Zhongzi No. 13”, which has an effective genome length of 274 Mb (http://www.ocri-genomics.org/Sinbase/), using the BWA software []. The mapping rate across different strains varied from 88.8% to 95.2%, for an average of 91.4%. The mapping result is consistent with that from the GATK software ( […]

Citations

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Sinbase institution(s)
Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture, China
Sinbase funding source(s)
This work was supported by the National Natural Science Foundation of China [No.31101182 and No.31371665]; the National Basic Research Program of China [973 Program, No. 2011CB109304]; and the National Crop Germplasm Resources Infrastructure [2013-014].

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