R/Shiny application for functional annotation of user-supplied FASTA sequences (nucleotide or protein).
Uses third-party tools including
- ESTScan to translate nucleotide sequences (if needed)
- 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) for best-hit extraction
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 the base URL.
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>
To use example FASTA files as input selections on the Funnotate home page (for example, to avoid having to hunt for them during a presentation), place them in your static/examples/ subdirectory.