| Manual panel |
| Home page |
 |
- Home: quick navigation; Search sites; Useful links; Introduction to
ArtocarpusGD; News; Cited publications.
- Genome: Details of 7 Artocarpus that genome-sequenced
genomes.
- Search & Tools: Tools intergrated in AGD: Search; Batch search (Batch cds and protein
sequnces); BLAST; JBrowse; Expression Heatmap; Synteny Viewer; Enrichment ; ArtocarpusCYC; MISAweb; Primer3.
- Family: Three aromatic related gene families(ADH/BAHD/TPS) on-line identification toolkit.
- Document: Statistics (data statistics of Artocarpus collected);
Resources (useful links).
- Community: manual (manual of accessing ArtocarpusGD); Download (genomic data files of
ArtocarpusGD).
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| Genome information page |
>>User can
browse genome detail of Artocarpus that collected in ArtocarpusGD, including
basic information, assembly status, genome annotation, and
publication. For each genome, this page contains hyperlink to tools
and downloadable genomic data.
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| Search page |
| Basic search |
>> Users can get
detail information by inputing putative genus or species, gene loci,
InterPro ID, GO term and KEGG ID.
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| Gene detail page |
>> Users can get
detail information by inputing putative gene loci.
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| Gene model page |
>> Users can get detail information by
clicking the gene model ID in gene detail page.
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| mRNA search page |
>> Users can get detail information of mRNA by
selecting the mRNA ID and corresponding species.
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| Batch search of mRNA and protein sequences |
>> Users can download the mRNA and
protein sequences from this function. Please select a Artocarpus genome and
feature type, and input transcripts, and then click the retrieve button.
Users can get the corresponding sequences from ArtocarpusGD.
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| Annotation search |
>> Users can Search Selected IDs' Annotation.
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| Blast page |
>> Users can Pefrom Blast Using Sequenceserver.
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| JBrowse page |
>> Users Can Get Detailed Information about Each Scaffold of Genome Using JBrowse Genome Browser.Furthemore, Can Got Expresson Heatmap by Clicking and Selecting on Each Sra ID
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| RNA-seq page |
>>User can select
reference genome, SRA, and input the gene list to get the gene expression in
the correspinding Artocarpus. By clicking the tag "Show example IDs", users can
get the demo gene list in the target Artocarpus genome.
>>This
is an heatmap of gene expression in the target Artocarpus genomes, and each gene
loci has a hyper-link to the page of gene detail.
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| Synteny Viewer page |
>> Users can Select "Genome",
"Chromosome/Scaffold" and "Choose a genome for comparison" in sequence, and click on the "Search" button to get the syntenic cirtlc gram on another html page.
>> Users can get detail information by
clicking the syntenic blocks on the circle gram.
>> Users can get detail information of every syntenic blocks.
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| GO enrichment |
>> Users can Select Genome Information and Corresponding mRNA/Protein ID for GO enrichment.
>> Users can get detail information by
clicking the gene model ID in gene detail page.
>> Users can get detail information by
clicking the gene model ID in gene detail page.
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| KEGG enrichment |
>> Performing Kegg Enrichment by Selected Species and Correspoding mRNA/Protein IDs.
>> Users Browse or Download KEGG Enrishment Results Table.
>> Users can get detail information by
clicking the gene model ID in gene detail page.
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| Family |
| ADH Family |
>> Users can try "case study", upload protein files or input sequences on line.
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>> Users can get identified ADH genes information, click on the geneID on the table can get detailed informations of each gene.
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| BAHD Family |
>> Users can try "case study", upload protein files or input sequences on line.
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>> Users can get identified BAHD genes information, click on the geneID on the table can get detailed informations of each gene.
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>> Users can download identified genes' ID and informations.
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| TPS Family |
>> Users can Identify Terpene Synthase Genes form Uploding Fies(Method1) or Inputting textfield(Method2).
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>>Identified TPS genes list, users also can download identified genes' ID and informations(txt/csv).
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| ArtocarpusCYC |
>> Users can click on every Genome for ArtocarpusCYC PGDBs.
>> Users can get detail information by
clicking each scaffold and can browse pathway detailed informations.
>> Users can get detail information of every metabolic pathway predicted by Pathologic.
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| Download page |
>> Gene page included
gene basic information, gene models. Gene model can
directly link to mRNA page in Artocarpus genome.
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