Database Creation, BlastP, Fetching Sequence

`sudo apt update`
`sudo apt install ncbi-blast+`

# Files needed

.pep file & .cds / .fasta file from Genome
.fasta file of query

# Step 1: Create a BLAST database
`makeblastdb -in #proteins.pep# -dbtype prot -out my_protein_db`

# Step 2: Run BLASTp search
`blastp -query #query.fasta# -db #my_protein_db# -out results.out -evalue 1e-5 -outfmt 7`

# Step 3: View the results
`cat results.out`

# Step 4: Sort Uniq IDS

`cut -f2 results.out | sort | uniq > subject_ids.txt`

To remove a range of lines (e.g., the first 3 lines):

`sed '1,3d' input.txt > output.txt`

# Step 5: Grab Sequence from .pep file Using Uniq ID

`seqtk subseq #database.pep# subject_ids.txt > extracted_sequences.fasta`

 `seqtk subseq ../saffron\ genome/Genome/crocus_sativus.gene.pep CsFT_ID.txt > extracted_csft_sequences.fasta`


# Step 6: To fetch the descriptions for a subset of IDs from a file containing IDs and their corresponding descriptions

`grep -Ff #subset_ids.txt# #id_description_file.txt# > matched_descriptions.txt`