# FAQ

## 1. How to use Prodigal to predict CDSs
1. Make sure that 'prodigal' is in your `PATH`.  
2. Set the option `--use_prodigal`.  
    When enabled, Prodigal will be used instead of the default prediction tool (MGA).
    
Note that Prodigal is not bundled in the DFAST distribution. Please install them by yourself. 


## 2. How to use tRNAscan-SE to predict tRNAs
1. Make sure that 'tRNAscan-SE' is in your `PATH`.  
2. Set the option `--use_trnascan [bact|arch]`.  
    `--use_trnascan bact` for bacterial genome, `--use_trnascan arch` for archaeal genome.  
    When enabled, tRNAscan-SE will be used instead of the default prediction tool (Aragorn).
    
Both tRNAscan-SE 1.3 and 2.0 can be used.  
Note that tRNAscan-SE are not bundled in the DFAST distribution. Please install them by yourself. 


## 3. What are the meanings of 'note' qualifiers in CDS features?
The note qualifier in GenBank or GFF format shows the result of an alignment to the reference sequence.
```
note="Q890K8 chromosomal replication initiator protein DnaA (Lactobacillus plantarum WCFS1)
[pid:65.2%, q_cov:99.8%, s_cov:99.8%, Eval:3.3e-166]"
```
`pid` and `Eval` represent percentage identity and E-value.  
`q_cov` and `s_cov` represents coverages against the query and subject (target) sequences, i.e. the percentages of the alignment length to the query and subject sequences, respectively.  
When either of `q_cov` or `s_cov` is below 70%, the alignment is marked as 'partial hit'.
When internal stop codons or frameshifts are found, they are also annotated in the note qualifier.  
  
`Q890K8` is an accession number of the reference sequence, and the following is its
description and, in parenthesis, the organism name from which it is derived.  
The accession numbers with 'WP_' come from the NCBI RefSeq database, and there are some from UniProt. This entry comes from UniProtKB [[Q890KB](https://www.uniprot.org/uniprot/Q890K8)].
