Lab 2 - Lavadav/EPP531_AGA GitHub Wiki
Introduction of Command Line (2)
1. Download the Arabidopsis Genome.
https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas.gz
2. Unzip/Decompress the file,
3. See What the genome looks like.
4. Count the number of chromosomes.
5. Download the Protein Sequences.
https://www.arabidopsis.org/download_files/Sequences/Araport11_blastsets/Araport11_pep_20220914.gz
Introduction to Blast.
6. Loading the program "Blast"
Download the Zebrafish protein sequences.
curl -o zebrafish.1.protein.faa.gz -L https://osf.io/68mgf/download
7. Make database for blast.
8. Run blast to compare "mgProteome.fasta" peptide sequence to Zebrafish database.
9. Discuss the results.
10. Run the same commands using program "Diamond".