Specific Use Cases

Recorded Sessions

1. Apollo basics (May 26 session):  https://us06web.zoom.us/rec/share/AbAWtFP-LUcs1OL1LszoH_WNnJsjKzbKYNW-XN414srWwR9ZUuKIl_IAQqiP9NPI.TSd77fNvC0-FfnWx
2. Apollo editing (June 29 session): https://us06web.zoom.us/rec/share/AXQB56B1l3xo8Z6wEYQLvu-60hR5OlvsR1yOwpKg1suhv4Yd_rPO7hHbzZeChARR.ol3bv8rmf7CHcf34
   

Slides

Apollo Basics Training Slides (May 23 and 26, 2023)

Apollo Editing Training Slides (May 31 and June 1, 2023)

Tab links

• Apollo
  • https://apollo-sandbox.arabidopsis.org/apollo/annotator/index

• Apollo Help Docs (longer, keep link handy):

  • https://genomearchitect.readthedocs.io/en/latest/UsersGuide.html

• NCBI Protein BLAST (use Reference proteins refseq_proteins as dataset)
  • https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE=Proteins&PROGRAM=blastp&PAGE_TYPE=BlastSearch&BLAST_SPEC=
• JBrowse
  • https://jbrowse.arabidopsis.org/index.html?data=Araport11&loc=Chr4%3A9054219..9058227&tracks=TAIR10_genome%2CA11-GL-Jan23%2CA11-PC-Jan23%2Cpollen_tophat%2Clight_tophat%2Cram_tophat%2Cleaf_tophat%2Cdark_tophat%2Csam_tophat%2Caerial_tophat%2Creceptacle_tophat%2Croot_tophat%2Cflower12_tophat%2Ccarpel_tophat&highlight=

Reading

• Grapedia materials (how to - general principles apply)
  • https://integrape.eu/resources/data-management/how-to-manually-curate-genes/
• Maize materials (how to - general principles apply)

• Apollo: Democratizing genome annotation (software summary and background)
  • https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006790

• Collaborative Annotation Redefines Gene Sets for Crucial Phytopathogens (see: 'Lessons Learnt for Future Collaborative Annotation Projects' section)
  • https://www.frontiersin.org/articles/10.3389/fmicb.2019.02477/full

• Application of a bioinformatics training delivery method for reaching dispersed and distant trainees (training background)

  • https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008715

• Double triage to identify poorly annotated genes in maize: The missing link in community curation (community annotation)

  • https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0224086
• Grapedia materials
  • https://integrape.eu/resources/data-management/how-to-manually-curate-genes/
• Maize materials
  • https://drive.google.com/drive/u/0/folders/19U84hdZm-wlQHhvCIWODGQOYy6jYOhlZ

• Apollo Help Docs (longer, keep link handy):

  • https://genomearchitect.readthedocs.io/en/latest/UsersGuide.html

Videos

Related Videos from Other Training Sessions in Other Organisms

General

Very detailed, lots of examples.

Changing intron/exon boundaries.