Amino Base Mapping (ABM)

Requirements

EMBOSS
sudo apt install emboss

SRA-Toolkit
sudo apt install sra-toolkit

How To Use

Allow file to execute as a program for :

• ABM_Detection.sh
• ABM_Mapping.sh
• revtrans.py
• search_pep.out

Peptide Mapping

-Copy the studied genome into the Genome folder (.fasta)
Compatible with : - Ensembl genome

-Run ABM_Mapping.sh with option -i as such :
sh ABM_Mapping.sh -i [peptide sequence]
Example : sh ABM_Mapping.sh -i VRIKPGSA

-Result in the Output/peptide_localisation.txt

Peptide Detection

Currently, Peptide Detection is limited to organisms with a genetic code similar to humans

-Go to https://www.ncbi.nlm.nih.gov/sra

-Create specific request.
Request example : "embryo[All Fields] AND (stem cells[All Fields] OR stem cell[All Fields]) AND transcriptome[All Fields] AND embryonic[All Fields] AND analysis[All Fields] AND "Homo sapiens"[Organism] AND ("biomol rna"[Properties] AND "library layout single"[Properties] AND "filetype fastq"[Properties])"

More info : https://www.ncbi.nlm.nih.gov/sra/docs/srasearch/

-Download SRA run IDs as "Runinfo"

-Run ABM_Detection.sh with options -i and -r as such :
sh ABM_Detection.sh -i [peptide sequence] -r [path_to_Runlist] -k(optional)

Example : sh ABM_Detection.sh -i VRIKPGSA -r Run_id.csv -k
sh ABM_Detection.sh -h for more info

-Result in the Output/transcriptome_result.txt