---
# System prepended metadata

title: bi278 lab3

---

# bi278 lab3
Exercise	1.	Annotate	a	genome	with	Prokka
1. Make	a	new	folder	for	lab_03 in	your	home	and	copy	one	of	the	genomes	(*.fasta)from	this week’s	folder
```
mkdir lab_03
cp /courses/bi278/Course_Materials/lab_03/P.bonniea_bbqs433.nanopore.fasta ./lab_03
```
2. Make	sure	you	know	your	new	genome’s	PATH by	checking	whether	you	can	find	it from	your current location	with	ls and	autocomplete.
```
ls
```
3. Run	Prokka annotation.	We	are	using	a	really	well	studied	genome	from	the	pathogenic	Burkholderia	pseudomallei as	a	closely	related	genome	to	improve	gene	prediction
```
prokka --force --outdir lab_03/bbqs433 --proteins /courses/bi278/Course_Materials/lab_03/Burkholderia_pseudomallei_K96243_132.gbk --locustag BB433 --genus Paraburkholderia --species bonniea --strain bbqs433 lab_03/P.bonniea_bbqs433.nanopore.fasta
```
## Q1
### .faa
Protein FASTA file of the translated CDS sequences.

### .ffn
Nucleotide FASTA file of all the prediction transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA). It contains different proteins and their corresponding gene

### .fna
Nucleotide FASTA file of the input contig sequences

### .gff
This is the master annotation in GFF3 format, containing both sequences and annotations. It can be viewed directly in Artemis or IGV.

### .txt
It contains the name of organism. number of contigs, number of bases, and number for CDS, CRISPR, rRNA, tRNA, tmRNA.

### .tsv
Tab-separated file of all features: locus_tag,ftype,len_bp,gene,EC_number,COG,product

## Q2
#### How	many CDS do	you	have?
I used the .txt file. Number of CDS is 3430

#### How	many	tRNA	do	you	have?
I used the .txt file. Number of tRNA is 56

#### How	many	'ribosomal	proteins'	do	you	have?
```
grep -c "ribosomal protein" PROKKA_09272022.tsv
```
I got 53.
#### How	many	‘hypothetical	proteins’ do	you	have?
```
grep -c "hypothetical protein" PROKKA_09272022.tsv
```
I got 1464.

## Q3
#### Which	file	is	the	most	useful	for	finding	genomic	locations	(chromosome	and	base	address)	of	 any	type	of	annotated	feature (genes (CDS),	tRNA,	etc)?
I think it should be the .gff file. Because in this file, there are information about the features (eg. CDS and the tRNA) with respect to which segment (location) of the genome. For example:
>1	Aragorn:001002	tRNA	32338	32413	.	+	.	ID=BB433_00027;inference=COORDINATES:profile:Aragorn:001002;locus_tag=BB433_00027;product=tRNA-Phe(gaa)

## Q4 
#### Compare	your	metrics	to	that	of	the	reference	genomes	for	these	two	species.	Are	your	results	similar?	Does	your	answer	impact	your	confidence	in	the	sequencing	quality	of	your	new	draft	genome?
I think the result is similar. At least for the tRNA part, my result is the same as the one on website. I think this result gives me more confidence in the quality of my draft genome. 