Ptua epiMOD Annotation

Author

Steven Roberts

Published

April 10, 2025

Peve

proteins

https://gannet.fish.washington.edu/seashell/snaps/Pocillopora_meandrina_HIv1.genes.pep.faa

cd ../data
curl -o Pocillopora_meandrina_HIv1.genes.pep.faa https://gannet.fish.washington.edu/seashell/snaps/Pocillopora_meandrina_HIv1.genes.pep.faa

head ../data/Pocillopora_meandrina_HIv1.genes.pep.faa

mkdir ../output/03-Ptua-epimods-blast/

/home/shared/ncbi-blast-2.15.0+/bin/makeblastdb \
-in ../data/Pocillopora_meandrina_HIv1.genes.pep.faa \
-dbtype prot \
-out ../output/03-Ptua-epimods-blast/Pocillopora_meandrina_HIv1.genes.pep

fasta="../data/Machinery.fasta"

/home/shared/ncbi-blast-2.15.0+/bin/blastp \
-query $fasta \
-db ../output/03-Ptua-epimods-blast/Pocillopora_meandrina_HIv1.genes.pep \
-out ../output/03-Ptua-epimods-blast/Mach-blastp-Ptua_out.tab \
-evalue 1E-05 \
-num_threads 48 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6

wc -l ../output/03-Ptua-epimods-blast/Mach-blastp-Ptua_out.tab

480 ../output/03-Ptua-epimods-blast/Mach-blastp-Ptua_out.tab

head ../output/03-Ptua-epimods-blast/Mach-blastp-Ptua_out.tab

Dnmt1-201   Pocillopora_meandrina_HIv1___RNAseq.g8948.t1    57.918  1345    517 16  294 1598    191 1526    0.0 1543
Dnmt3a-201  Pocillopora_meandrina_HIv1___RNAseq.g2960.t2    48.233  651 294 7   286 905 78  716 0.0 621
Dnmt3b-201  Pocillopora_meandrina_HIv1___RNAseq.g2960.t2    43.776  715 322 12  181 857 44  716 0.0 596
Dnmt3l-201  Pocillopora_meandrina_HIv1___RNAseq.g16036.t1   58.795  1859    717 17  453 2289    1   1832    0.0 2202
USP9Y-201   Pocillopora_meandrina_HIv1___RNAseq.g16036.t1   58.297  1832    714 17  30  1838    27  1831    0.0 2143
USP10-201   Pocillopora_meandrina_HIv1___RNAseq.g12276.t1   47.193  481 210 15  338 798 366 822 1.53e-127   401
USP11-201   Pocillopora_meandrina_HIv1___RNAseq.g19447.t1   45.005  931 442 19  62  935 2   919 0.0 733
USP12-201   Pocillopora_meandrina_HIv1___RNAseq.g18898.t1   74.255  369 78  3   16  369 1   367 0.0 563
USP14-201   Pocillopora_meandrina_HIv1___RNAseq.g22603.t1   62.805  492 168 4   1   487 1   482 0.0 646
USP15-201   Pocillopora_meandrina_HIv1___RNAseq.g19447.t1   53.340  943 387 15  5   934 13  915 0.0 954