From genomes to GIFT evidence
giftag annotates genome and protein FASTA files with the markers that gifter evaluates.
GENOME ANNOTATION · THE FIRST STEP IN A GIFT ANALYSIS
Get started See the handoff to gifter
One traceable path
giftag builds a local profile database from the marker list in gifter’s curated reference database. It searches KOfam, NCBIfam, Pfam and dbCAN profiles using each source’s acceptance rule, then writes one row per gene and accepted marker. The row includes the score, threshold, profile and source behind the observation.
The marker table goes straight into gifter. gifter applies its curated completeness models and reports which capabilities have genomic support, which requirements are missing and which genes supplied the evidence. A marker hit by itself is not a GIFT call.
Start with a genome
giftag build
giftag annotate -i genomes/example.fa.gz -o annotations/markers <- read.delim("annotations/giftag_markers.tsv")
calls <- gifter::evaluate_gifts_community(markers)The first command downloads and compiles a local database. Read Get started before running it: the sources have their own terms, and the full build downloads about 2.9 GB. The example path is illustrative; giftag accepts multiple FASTA files or a directory.
WHERE THE TOOLS MEET
giftag observes markers; gifter evaluates capabilities. Keep giftag_run.json and the database manifest with your results so the source releases, gifter database version and search settings remain traceable.