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Contents

1. Home

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Home: Welcome to Sinbase2.0; News in Sinbase2.0; Flowchart for Multi-Omics Data Integration; Genome Version; Summary; Statistics of Visitors. Resource: Genomics; Genetics Linkage Analysis; Comparative Genomics; Transcriptomics Analysis; Proteomics Analysis. Tools: General Search; Advanced Search; MISAweb; Genome Browser. Document: Statistics; Links; Publications. Help: Download; Manual. FAQ: FAQ.

 

2. Genomics

2.1 Genome Components

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Users can click chromosome bar to get the basic information of interested chromosomes in Sesamum indicum genome. When the mouse moved on the scope of chromosome bar, the system will popup a tooltip and then users can click the corresponding scope of interested chromosomes to get corrsponding genome components.

 

2.2 Functional Annotation

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Users can click the numbers which were added hyperlinks to get the annotated genes by public open-resource databases and the involved terms from public open-resource databases. From this section, users can get the function of interested genes or the gene sets from the same terms from public open-resource databases.

 

3. Genetics Linkage Analysis

3.1 SLAF Linkage Group

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Users can click the gene list to get upstream and downstream flanking genes of corresponding sesame SLAF markers by GBrowse software.

3.2 Bin Map

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Users can click the gene list to get upstream and downstream flanking genes of corresponding sesame bin by GBrowse software.

3.3 SSR Linkage Group

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Users can click the interested chromosome to get the list of SSR markers in corresponding chromosomes in Sesamum indicum genome. After getting the list of SSR markers, users can get basic information of each SSR marker in Sesamum indicum genome.


4. Comparative Genomics

4.1 Intra-species Comparison

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Users can click the numbers which were added hyperlinks to get the list of anchored scaffolds or contigs from Sesamum indicum var. Yuzhi11, Swetha, Baizhima and Mishuozhima on the chromosomes in Sesamum indicum var. Zhongzhi13 genome. After getting the list of anchored scaffolds or contigs from other varieties, users can get basic information of each anchored scaffold or contig on the chromosomes in Sesamum indicum genome.


4.2 Interspecies Comparison

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Users can click the numbers which were added hyperlinks to get interested collinear genomic regions about interspecies comparative genomics analysis in Arabidopsis thaliana, Vitis vinifera, Solanum tuberosum, Solanum lycopersicum, Sorghum bicolor, Oryza sativa compared with Sesamum indicum genomes. After getting the list of collinear genomic regions among 6 species with Sesamum indicum genome, users can get basic information of each collinear genomic region between Sesamum indicum and another one genome.

 

5. Genomic Variation Analysis

5.1 SNP Annotation

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Users can select two ways to get SNP information on different sesame chromosomes including setting ranges and scales on chromosome.

6. Transcriptomics Analysis

6.1 Waterlogging Resistance

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Users can click the numbers which were added hyperlinks to get expression values of expressed genes among different samples in Sesamum indicum under waterlogging resistance. For co-expression analysis, users can click the scope of co-expressed block to get co-expressed genes under waterlogging resistance.

 

6.2 Drought Tolerance

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Users can click the numbers which were added hyperlinks to get expression values of expressed genes among different samples in Sesamum indicum under drought tolerance. For co-expression analysis, users can click the scope of co-expressed block to get co-expressed genes under drought tolerance.


6.3 Three Color Seeds

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Users can click the numbers which were added hyperlinks to get expression values of expressed genes among different color seeds in Sesamum indicum. For co-expression analysis, users can click the scope of co-expressed block to get co-expressed genes from different color seeds.


6.4 Determinate and Indeterminate

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Users can click the numbers which were added hyperlinks to get expression values of expressed genes among different samples in Sesamum indicum. For co-expression analysis, users can click the scope of co-expressed block to get co-expressed genes from different phenotypes of determinate and indeterminate growth habits in Sesamum indicum.


6.5 Seed Development

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Users can click the numbers which were added hyperlinks to get expression values of expressed genes among different samples in Sesamum indicum. For co-expression analysis, users can click the scope of co-expressed block to get co-expressed genes from different samples.


7. Proteomics Analysis

7.1 Salt Tolerance

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Users can click the numbers which were added hyperlinks to get expression quantifications of expressed proteins among different samples in Sesamum indicum. For protein-protein interaction analysis, users can click the "Interactive network" to get interactive networks from different samples.


8. Markers, Genes and QTLs

8.1 Functional Markers

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Users can click the locaton to get upstream and downstream flanking genes of corresponding sesame functional marker by GBrowse software.

8.2 Functional Genes

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Users can click the gene name to get detail information of corresponding sesame functional gene in Sinbase2.0.

8.3 Functional QTLs

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Users can click the locaton to get gene list containing corresponding sesame functional QTL by GBrowse software.

Copyright © 2017 Sesame Germplasm Resources Group, OCRI, CAAS, Admin: yujingyin@caas.cn