Week 4 Lab

#1
wget https://www.arabidopsis.org/download_files/Genes/TAIR10_genome_release/TAIR10_chromosome_files/TAIR10_chr_all.fas.gz

#2
gunzip TAIR10_chr_all.fas.gz

#3
less TAIR10_chr_all.fas

#4
cat TAIR10_chr_all.fas | grep ">" | wc -l

#5
wget https://www.arabidopsis.org/download_files/Sequences/Araport11_blastsets/Araport11_pep_20220914.gz

#6
curl -o zebrafish.1.protein.faa.gz -L https://osf.io/68mgf/download

#7
gunzip zebrafish.1.protein.faa.gz
spack load blast-plus
makeblastdb -in zebrafish.1.protein.faa  -dbtype prot

#8 
blastp -query ../Commandline_Lab/Data/mgProteome.fasta -db zebrafish.1.protein.faa -out zebravsMG.txt

#9
less zebravsMG.txt

#10
spack load [email protected]
diamond makedb --in zebrafish.1.protein.faa -d zebrafish
# this did not work
diamond blastp -q Araport11_pep_20220914 -d zebrafish.dmnd -o ArabidopsisvsZebrafish
# so i used this instead
diamond blastp -q ../Commandline_Lab/Data/mgProteome.fasta -d zebrafish.dmnd -o ArabidopsisvsZebrafish