Genome Annotation Service


Genome Annotation Service Overview

The Genome Annotation Service uses the RAST tool kit (RASTtk) to provide annotation of genomic features. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions (the batch submission interface will be made available in PATRIC in future release).


Using the Genome Annotation Service

NOTE: You must be logged into the PATRIC Workspace to use the Genome Annotation Service. Refer to Workspace and Groups for more information about logging into and using the workspace.

The PATRIC Genome Annotation Service can be accessed from the Services Menu at the top of the PATRIC website page:

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This will open the Genome Annotation Service input form page where you can enter the required information to annotate your genome.

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Parameters

Contigs – Upload the target FASTA file containing the genome sequence to annotate.

Domain – Choose the taxonomic domain of the target organism: bacteria or archaea.

Organism Name – Type or select an organism name. If the target species or strain is not listed select the most specific, accurate taxonomic level available.

Taxonomy ID – This field will auto-fill with the NCBI Taxonomy ID associated with the selected Organism Name.

Genetic Code – Choose the appropriate codon translation used for calling genes.

Output Folder – Select the desired workspace folder to send the results.  The default output folder is “home,” which is the root folder.

Output Name – Enter a desired name for the results file.

Uploading a Contig File

The Annotation Service accepts FASTA files (typically .f, .fasta, or .fna) as input. GenBank-formatted files are not currently accepted.  Before you can run the annotation service, a FASTA file must be uploaded. This can be performed from the workspace or by clicking the small folder next to the Contigs field on the Annotation Service page. When uploading a FASTA file to be annotated, designate it as a “contigs” object. To select a contig object after uploading, click the folder icon beside the Contigs field or using the drop-down arrow.

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Annotating the Genome

Once all the fields in the form are completed, click the Annotate button. This will queue the file as a “job” for the Annotation Service to process.

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Click on “Jobs” in the bottom right corner of the workspace to see the entire job list and status

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Once the annotation job has successfully completed, the output file with the name you selected will now appear in your workspace.  You can download this file from the workspace if desired.

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