liuyongcds / PhageRank

A suite for M13 phage display data analysis

PhageRank - A suite for M13 phage display NGS data analysis.

Authors: Taejoon Kwon ([e-mail])

Phage M13 Genomes

• PhageM13_genome.V00504.fa - from https://www.ebi.ac.uk/ena/browser/view/V00604.2
• PhageM13_genome.JX412914.fa - from https://www.ebi.ac.uk/ena/browser/view/JX412914.1

Phage M13 variable region for screening

• Green: a variable region (12 amino acids == 36 nucleotides)
• Red: a target of PhageM13_ILMN_F
• Orange: a target of PhageM13_ILMN_R
• Yellow/Cyan : a pair of reads with 2x150bp sequencing (a bold hexamer will be dropped due to the UMI).

Primers for Phage M13 variable region amplification & the library prep.

• Nextera_i5, Nextera_i7 - a pair of conventional Illumina Nextera barcode adapters.
• PhageM13_ILMN_F & PhageM13_ILMN_R - a pair of primers for phage M13 variable region amplification.
• 'NNNNNN' - a hexamer used for UMI (to estimate the amplification bias)

Ref

• ipcress (for in silico PCR): https://www.ebi.ac.uk/about/vertebrate-genomics/software/ipcress-manual