Rhodnius manual annoation

Here are some useful links for the Rhodnius manual annotation resources:

Back to the Portal main page

Documents:

• Quick manual annotation tutorial (pdf) abridged Portuguese tutorial (pdf)
• Still confused? See our annotation decision tree picture, with clickable links!
• Explanation of the features in the extended downloadable GFF3 from the data portal
• Description of the automated annotation process (pdf)

VectorBase resources:

• Access the genome browser
• BLAST the genome, transcripts and proteins
• Form to download gene models or fasta sequences (gene models in GFF3 include extensive supporting evidence)
• Form to submit gene models
• Form to delete or approve a gene, comment, add gene symbol/description or set as pseudogene

​Downloads:

• Fasta sequences: transcripts, peptides and supercontigs 
• Geneset: GFF3 and GTF (only the VectorBase gene models)
• Plus InterPro and GO annotation: protein domains, InterPro annotation, GO annotation
• Orthology & paralogy information from OrthoMCL: 'raw' output, spreadsheet with links to genome browser
• Genes with isssues spreadsheets: unsupported, dubious, problematic, documentation

Annotation Editors:

• Apollo genome annotation viewer and editor
  • Apollo user guide 
  • Apollo tutorial
• Artemis genome browser and annotation tool
  • Artemis manual
  • Artemis course (pdf)

Program:

• The Windows program GffTool.exe splits the GFF file into annotated genes and supporting evidence. It also does a quick check on the GFF before submission.
  • To use it, go to start and then run and type in cmd the program name split and the file name e.g. GffTool.exe split my_GFF_file.gff
  • E-mail DanH (cap_qc@vectorbase.org) for any comments
• If you're using Unix/Linux or Mac, use a basic grep to extract the annotated genes and supporting evidences:
  • To get annotations: grep "VectorBase" my_GFF_file.gff > my_GFF_annotation.gff
  • To get supporting features: grep -v "VectorBase" my_GFF_file.gff > my_GFF_supporting-features.gff

Frequently Asked Questions

Contact us (cap_qc@vectorbase.org) if you have any questions regarding the manual annotation process.

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