prokka-genome-annotation

To annotate a prokaryotic genome, this Skill identifies protein-coding genes, tRNAs, and rRNAs using Prodigal. It assigns functional annotations by searching against databases like Pfam and RefSeq to help you understand gene functions.

Genome annotation outputs are generated in standard formats including GFF3, GenBank, FASTA, and TSV. These files contain the identified genetic features and functional assignments needed for downstream comparative genomics analysis.

Prokaryotic genome annotation supports bacteria, archaea, and viruses. It uses bioinformatics tools like BLAST and HMMER to identify genes and assign functions across these different microbial genome types.

The best way to predict protein-coding genes rapidly is by using Prodigal within an automated genome annotation workflow. This process identifies CDS regions and assigns functions by comparing them against the TIGRFAMs database.

You need a genome assembly in FASTA format to start genome annotation. The Skill processes this FASTA file to predict genes and outputs the results to a specified directory with your chosen prefix.

Automated functional annotation uses multiple databases like Pfam, TIGRFAMs, and RefSeq to maximize the accuracy of gene function assignment. Searching against these distinct profiles ensures comprehensive coverage for prokaryotic genomics.