Funnotate
R/Shiny application for functional annotation of user-supplied FASTA sequences (nucleotide or protein).
Uses third-party tools including
- ESTScan to translate nucleotide sequences
- BLAST alignment to reference gene databases (soybean, Medicago, Arabidopsis)
- InterProScan (methods: TIGRFAM, SMART, SUPERFAMILY, Gene3D, PIRSF, Pfam, Coils)
- HMMer for assigning gene family
- AHRD - Automated Human Readable Descriptions
Clicking a 
icon in the Gene Family column of the summary table calls Lorax to compute that family’s phylogenetic tree. The resulting Phylogram page visualizations use these JavaScript libraries:
View the application here.
To review a previously uploaded sequence set (for example, to launch a new annotation job), append ?upload=<upload_index>
To review an existing annotation job, append ?job=<job_id>
To view the phylogram for a gene family with sequences inserted by an existing job, append ?family=<family>&job=<job_id>
To view the phylogram for a gene family alone (with no user-supplied sequences), append ?family=<family>
To additionally highlight the proteins associated with specified genes from that family, append ?family=<family>&gene_name=<gene1>,<gene2>,<...>,<geneN>
To automatically determine the gene family associated with one or more specified genes, append ?gene_name=<gene1>,<gene2>,<...>,<geneN>
If this finds more than one unique gene family, it will display the results in a table. Choose one to display its phylogram, with any related proteins highlighted.
To search for gene families by functional keywords, append ?search or ?search=<keywords>