Contents
How does Prokka work?
Prokka is a “wrapper”; it collects together several pieces of software (from various authors), and so avoids “re-inventing the wheel”. Prokka finds and annotates features (both protein coding regions and RNA genes, i.e. tRNA, rRNA) present on on a sequence.
What is sequencing annotation?
Sequence annotation is the process of marking specific features in a DNA, RNA or protein sequence with descriptive information about structure or function.
When to use Rast for genome annotation?
The approach that we advocate is especially suited to annotating a genome that is quite phylogenetically close to an existing (presumably, well-annotated) genome or set of genomes. In particular, it works well for newly-sequenced pathogen genomes that are close to large groups of already sequenced genomes. The proposed approach is as follows:
How to use prokka to annotate a genome?
Here we introduce Prokka, a command line software tool to fully annotate a draft bacterial genome in about 10 min on a typical desktop computer. It produces standards-compliant output files for further analysis or viewing in genome browsers.
Which is better, prokka, RAST or xbase2?
Prokka was designed to be both accurate and fast. To assess accuracy, we compared the annotations of Prokka, RAST and xBase2 for the highly curated Escherichia coli K-12 genome. All methods were told it was an E.coli genome. Table 3 shows that Prokka produced an overall better annotation than both RAST and xBase2.
How to use prokka to annotate jy1305contig.fasta?
Here what you are asking prokka to do is annotate the contigs in JY1305contig.fasta, name the contigs as if from a sequencing center named “U”, make the annotations compliant with NCBI standards (necessary if you want other tools to read your files) and force an overwrite of previous iterations of a default-named output directory.