Prokaryotic genome assembly and sequencing has a mature methodology, but there is no fast and easy way to annotate the assembled genome.

Prokka: rapid prokaryotic genome annotation is a fast and efficient automated annotation tool for prokaryotic genomes, which takes pre-assembled genome DNA sequences in FASTA format as input files, and is capable of fast and efficient functional annotation of prokaryotic genomes and macrogenomes, identifying and labeling all relevant features on the genome sequence. It is capable of rapid and efficient functional annotation of prokaryotic genomes and macrogenomes, and identifying and labeling all relevant features on genomic sequences.

Operation method

Prokka annotated prokaryotic genomes

Materials and Instruments

The assembled bacterial genome fasta file, e.g. .fa

Move

1. Dependent installation on Linux environment: conda install prokka

2. Activate the software in your environment: conda activate /path/prokka

3. Check the parameters: prokka -h

4. Run:

prokka [options] <filename.fasta>

5. View the results:

.gff Gene annotation file

.gbk Genebank format annotated file

.fna Input nucleotide sequence file

.faa Translated amino acid sequence of CDS (coding region)

.ffn Nucleotide sequence of all transcript annotations

.sqn Sequence in editable format for submission

.fsa Nucleotide sequence for submission

.tbl Characterization table file for submission

.err Suspicion or error reporting

.log Runtime log

.txt Statistics for all types of annotated sequences

.tsv List of all annotated gene features

Caveat

1. Prefix the software with the original path:2. activate conda environment before use: conda activate path/prokka3. ftype defaults to CDS, using the addgenes or addgmma parameter will differentiate between coding genes or RNA.

For more product details, please visit Aladdin Scientific website.

https://www.aladdinsci.com/