# To search for joined exons of gene-coding sequences in S. palustre
# starting from an amino acid sequence, copy the genome-containing
# FASTA file named "Spalustre_genome.fasta" in this folder to your local
# folder. Then, run:

ml Exonerate
exonerate --model protein2genome --query <protein_sequence.fasta> --target Spalustre_genome.fasta --showvulgar no --showalignment no --ryo ">%ti %tab %tae %pi\n%tcs\n" > exonerate_output.txt

# where <protein_sequence.fasta> is a file containing the amino acid sequence in FASTA format. For example:
# >proteinID
# AVGHTYAASVKPPEWTYGGGCDSVV