Specific Use Cases

Recorded Sessions

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

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

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

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=

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)

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

General

Very detailed, lots of examples.

Changing intron/exon boundaries.