Blast practice
Blast practice
Blast with NCBI
- Go to NCBI
- Click
Protein BLAST
- upload
sopD_proteinfasta
file, choose the databaseswissprot
, clickAlgorithm parameters
at the bottom, check all the options. ClickBLAST
- The BLAST may run for a while. Check the results:
- How many hits are there?
- Check the
Query cover
,E value
,Per. Idet
. How many hits have a E-value lower than 10e-6? What does this mean? - Click the second alignment. How many
Identities
,Positives
andGaps
?
Run a local Blast
- Use
Filezilla
, uploadsopD_gene.fasta
,salmonella_typhimurium_lt2.fasta
to server. -
Run
Blast
from your conda virtual environment:conda activate bioinfo makeblastdb -in sopd_gene.fasta -dbtype nucl -out sopD blastn -query salmonella_typhimurium_lt2.fasta -db sopD -out sopD_lt2.txt -outfmt 1
Read the
help
document of each program before you run it. Make sure you understand all the parameters you typed in.After the program completes, read the output file
sopD_lt2.txt
Try another output format:
blastn -query salmonella_typhimurium_lt2.fasta -db sopD -out sopD_lt2_fmt6.tsv -outfmt 6
Visualise the blast results
- Run
act
on your laptop - Click
File
-Open
, opensopd_gene.fasta
as sequence 1,sopD_lt2_fmt6.tsv
as comparison file,salmonella_typhimurium_lt2.fasta
as sequence 2. - When the
act
window open, use the scrollbar at top-right to zoom in. Double click the red bar in the middle, to put the match sequence in the center. What is the position of Salmonella Typhimurium genome that matches the sopD gene?