Phage Display

PhIP-Seq Characterization of Serum Antibodies Using Oligonucleotide Encoded Peptidomes

Divya Mohan, Daniel L. Wansley, Brandon M. Sie, Muhammad S. Noon, Alan N. Baer, Uri Laserson, and H. Benjamin Larman

My implementation script

#!/usr/bin/env bash
#
#	python3 -m pip install --upgrade --user numpy scipy biopython==1.69 click tqdm pepsyn phip-stat
#
#	http://weizhong-cluster.ucsd.edu/cd-hit/
#	https://github.com/weizhongli/cdhit/releases
#	wget https://github.com/weizhongli/cdhit/releases/download/V4.8.1/cd-hit-v4.8.1-2019-0228.tar.gz

TILESIZE=$1
OVERLAP=$2
INPUT=$3

cat ${INPUT} \
	| pepsyn x2ggsg - - \
	| pepsyn tile -l $TILESIZE -p $OVERLAP - - \
	| pepsyn disambiguateaa - - \
	> orf_tiles-${TILESIZE}-${OVERLAP}.fasta

cat ${INPUT} \
	| pepsyn x2ggsg - - \
	| pepsyn ctermpep -l $TILESIZE --add-stop - - \
	| pepsyn disambiguateaa - - \
	> cterm_tiles-${TILESIZE}-${OVERLAP}.fasta

~/.local/cd-hit-v4.8.1-2019-0228/cd-hit \
	-i orf_tiles-${TILESIZE}-${OVERLAP}.fasta \
	-o orf_tiles_clustered-${TILESIZE}-${OVERLAP}.fasta \
	-c 0.95 -G 0 -A 100 -M 0 -T 1 -d 0

~/.local/cd-hit-v4.8.1-2019-0228/cd-hit \
	-i cterm_tiles-${TILESIZE}-${OVERLAP}.fasta \
	-o cterm_tiles_clustered-${TILESIZE}-${OVERLAP}.fasta \
	-c 0.95 -G 0 -aL 1.0 -aS 1.0 -M 0 -T 1 -d 0


cat orf_tiles_clustered-${TILESIZE}-${OVERLAP}.fasta \
	cterm_tiles_clustered-${TILESIZE}-${OVERLAP}.fasta \
	| pepsyn pad -l $TILESIZE --c-term - - \
	> protein_tiles-${TILESIZE}-${OVERLAP}.fasta


PREFIX=AGGAATTCCGCTGCGT
SUFFIX=GCCTGGAGACGCCATC
PREFIXLEN=${#PREFIX}
SUFFIXLEN=${#SUFFIX}
FREQTHRESH=0.01

cat protein_tiles-${TILESIZE}-${OVERLAP}.fasta \
	| pepsyn revtrans --codon-freq-threshold $FREQTHRESH --amber-only - - \
	| pepsyn prefix -p $PREFIX - - \
	| pepsyn suffix -s $SUFFIX - - \
	| pepsyn recodesite --site EcoRI --site HindIII --clip-left $PREFIXLEN \
	--clip-right $SUFFIXLEN --codon-freq-threshold $FREQTHRESH \
	--amber-only - - \
	> oligos-${TILESIZE}-${OVERLAP}.fasta


pepsyn findsite --site EcoRI --clip-left 3 oligos-${TILESIZE}-${OVERLAP}.fasta

pepsyn findsite --site HindIII oligos-${TILESIZE}-${OVERLAP}.fasta


pepsyn clip \
	--left $PREFIXLEN \
	--right $SUFFIXLEN \
	oligos-${TILESIZE}-${OVERLAP}.fasta \
	oligos-ref-${TILESIZE}-${OVERLAP}.fasta


#	bowtie-build -q oligos-ref.fasta bowtie_index/mylibrary

20231227 - I've created an entire repo for this project

https://github.com/ucsffrancislab/PhIP-Seq