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GhostKOALA

Step-by-step Instructions



Step 1. Query data input

Enter three items: query sequence data, database file to be searched, and your email address. Then click on "Request for email confirmation".
When your request is successfuly uploaded, a message of "Requested accepted" will appear. Check that your email address is correctly entered.
Request accepted

An email has been sent to xxxxxx@xxxx.xxx.xx for confirmation.

Please click on the link in the email to submit your GhostKOALA job.

Step 2. Job submission

Check your mailbox. You should immediately receive an email from the GhostKOALA server located at the Supercomputer Facility in the Institute for Chemical Research, Kyoto University (scl.kyoto-u.ac.jp).

Your GhostKOALA job request
  Query dataset: 3123 entries
  KEGG database to be searched: genus_prokaryotes.pep


Please click on the link below to either submit or cancel your job.

http://www.kegg.jp/kegg-bin/blastkoala_submit?id=xx..&type=ghostkoala (Submit)

http://www.kegg.jp/kegg-bin/blastkoala_cancel?id=xx..&mode=cancel&type=ghostkoala (Cancel)

If no action is taken within 24 hours, your request will be deleted.

Click the submit link in the message to submit your job. Your job will be queued on the GhostKOALA server. The execution time varies depending on how many other jobs are running.

Step 3. Accessing result data

When your job is completed, you will receive a notification email.
Your GhostKOALA job was completed.

Please click on the following link to view the result of annotation.

http://www.kegg.jp/kegg-bin/blastkoala_result?id=xx..&type=ghostkoala

Your result data will be removed after seven days.
Click on the link in the message to access your result summary page, which consists of two sections: Annotation data (and KEGG Mapper) and Taxonomy data.
Your GhostKOALA job
Query dataset: 567036 entries
KEGG database searched: c_family_euk+genus_prok+viruses
Job submitted: Thu Mar 12 13:48:20 JST 2015
Job completed: Thu Mar 12 15:25:16 JST 2015

Annotation dataPreview first 100 | Download
Summary
267496 entries (47.2%) annotated
Functional
category
(Pie chart)
KEGG MapperReconstruct Pathway
Reconstruct Brite
Reconstruct Module
Taxonomy dataPreview first 100 | Download
Taxonomic
category
(Pie chart)
More details
View all taxonomic categories (and perform KEGG Mapper analysis)
For the annotation data section, you can download the annotation data (K number assingments) and perform KEGG Mapper analysis for the entire metagenome. The pie chart shows the functional category defined by the KEGG Orthology system. Click on "Preview first 100" to see how the downloaded file looks like. It is a tab-delimited file consiting of your query gene ids with assigned K numbers and their definitions.

For the taxonomy data section, you can examine taxonomic compositions of metagenome data and perform KEGG Mapper analysis by distinguishing taxonomic groups. The pie chart shows the taxonomic category defined by the third level of the KEGG Organisms hierarchy. Click on "Preview first 100" to see how the downloaded file looks like. For each query gene it contains taxonomic information of the top hit gene in the KEGG GENES database in the form summarized below.
Column1User's gene id
Column2K number assinged
Column3Second level of the KEGG Organisms hierarchy
Column4Third level of the KEGG Organisms hierarchy
Column5Genus in the NCBI taxonomy
Column6KEGG GENES ID
Column7GHOSTX score
Note that the pie chart for the second level of the KEGG Organisms hierarchy is generated by using the cutoff GHOSTX score of 100. You may use different thresholds by manipulating the dowloaded file.

Click on "View all taxonomic categories" to open a new page where you can select KEGG organism groups in the third or the second level and perform "Reconstruct Pathway" and "Reconstruct Brite" analyses either directly from this page or using KEGG Mapper pages through generated mapper files.

Step 4. Feedback and citation

We welcome your comments and suggestions, especially on any addition or correction of gene/protein function annotation with relevant reference information. Please use the KEGG/GenomeNet Feedback Form.

Please cite the following reference when you make use of BlastKOALA/GhostKOALA.

Last updated: December 21, 2015

[ GhostKOALA | KEGG | Kanehisa Labs ]