reciprocal blast

Peach vs sweet cherry

Analysis is stored in <your_project_directory>

• peach protein fasta sequences download from phytozome
• cherry protein fasta sequences download from GDR

build blast database

spack load [email protected]

makeblastdb -in protein_fasta_file -dbtype prot

-in input file.
-dbtype input file format (nucleotide sequences as nucl, protein sequences as prot).

blast peach against cherry

spack load [email protected]

blastp \
	-query <peach_protein_sequence.fasta> \
	-db <cherry_protein_sequence.fasta> \
	-out <your_output_file.txt> \
	-evalue 1e-5 \
	-outfmt 6 \
	-max_target_seqs 1 \
	-num_threads 10

-quary input sequences. -db reference sequences.
-out output file.
-evalue evalue cutoff.
outfmt output format. 6 means a tab separate format.
-max_target_seqs keep one hit (one of the best hit).
-num_threads number of cores will use to run this program.

blast cherry against peach

Use cherry sequences as query and peach sequences as reference. Run the same blastp command as above.

Best reciprocal blast hits

There is a python script we can use. We will try it once we get there.