Data, code, and results for our paper Standardized genome-wide function prediction enables comparative functional genomics: a new application area for Gene Ontologies in plants (https://doi.org/10.1093/gigascience/giac023). If you use any of our code or results in a scientific publication, we would be grateful if you cite the paper.
Use the complete sequence ID in the fasta files as the ids for GOMAP, then replace the column 2 (Object Symbol) in the resulting GAF with something shorter (e.g. gene locus)
remove the asterisks at the end of the sequences
use the primary sequence if they have one instead of the longest transcript
Thyra
commented
2 years ago
Genomes
Decisions
Use the complete sequence ID in the fasta files as the ids for GOMAP, then replace the column 2 (Object Symbol) in the resulting GAF with something shorter (e.g. gene locus)
remove the asterisks at the end of the sequences
use the primary sequence if they have one instead of the longest transcript
put LIS(legumeinfo.org/data) as DB in column 1
[ ] Prepare input and config
[x] Seqsim
[ ] Domain
[x] fanngo
[x] blast
[x] preproc
[ ] mixmeth
[ ] aggregate
Then publish on Cyverse:
[ ] submit for DOI
[ ] make sure everything is correct
Then send to Steven: