Peptide Parameter Generator

This is a bash script that generates the count of aromatic, polar, non polar, acidic and basic residues from a text file containing the peptide sequences.

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The amino acids were classified according to the following guideline. This is taken from Lehninger Principle of Biochemistry. Courtesy of @Minhas Hossain Sakib

Instructions:

• Download the paramgen.sh file or clone the repository
• Copy all your peptides sequences in a text file

• Place it in the same folder as the paramgen.sh file
• Open a terminal and navigate to the folder where the the script and text file is located or open a terminal directly from the location of the folder
• Make the paramgen.sh script executable (if not already) by typing

chmod +x paramgen.sh

• Finally, run the script by typing

# ./paramgen.sh <type_your_filename>
# For example if you saved the peptide sequences in peptides.txt file
./paramgen.sh peptides.txt

• A tsv file will be generated named peptide_param.tsv
• Open the file in excel

Sequence	Length	Aromatic	Negatively Charged	Positively Charged	Polar	Non-polar
GIPCAESCVYIPCTVTALLGCSCSNRVCYN	30	2	1	1	13	13
GIPCGESCVWIPCISSAIGCSCKSKVCYRN	30	2	1	3	12	12
GIPCGESCVWIPCLTSAIGCSCKSKVCYRN	30	2	1	3	12	12
GIPCGESCVWIPCISSAIGCSCKNKVCYRN	30	2	1	3	12	12
GTPCGESCVWIPCISSAVGCSCKNKVCYKN	30	2	1	3	11	13
GTLPCGESCVWIPCISAVGCSCKSKVCYKN	30	2	1	3	12	12
SIPCGESCVWIPCTITALAGCKCKSKVCYN	30	2	1	3	12	12
GTLPCESCVWIPCISSVVGCSCKSKVCYKN	30	2	1	3	11	13
GLPVCGETCVGGTCNTPGCTCSWPVCTRN	29	1	1	1	12	14
FRGLAKLLKIGLKSFARVLKKVLPKAAKAGKALAKSMADENAIRQQNQ	48	2	2	12	25	7
GKFSGFAKILKSIAKFFKGVGKVRKQFKEASDLDKNQ	37	5	3	10	13	6
GKLSGISKVLRAIAKFFKGVGKARKQFKEASDLDKNQ	37	3	3	10	15	6
GKFSVFSKILRSIAKVFKGVGKVRKQFKTASDLDKNQ	37	4	2	10	13	8
GFGALFKFLAKKVAKTVAKQAAKQGAKYVVNKQME	35	4	1	8	17	5
GFGSLFKFLAKKVAKTVAKQAAKQGAKYIANKQME	35	4	1	8	16	6

• Enjoy !!

Hello, This is Maruf Ahmed Bhuiyan

I am a doctor by profession and a researcher by passion. I am currently pursuing my Doctor of Medicine (MD) in Virology in the Department of Virology at Bangabandhu Sheikh Mujib Medical University. I am passionate about impactful research and constantly on the hunt to acquire new skills.

• I are currently working on Genomics, Vaccinomics, Computer Aided Drug Design, Machine Learning, Data Analaysis, Interactomics

• Ask me about Anything Science! I am passionate about talking science

• How to reach me? dr.maruahmed89@gmail.com

• My webste: www.marufahmed.carrd.co

• Fun fact: I Love Programming