Serpent

Explore DNA data with Serpent

Serpent is an exploration into DNA and RNA sequences, nucleotide bases, codons, amino acids and genome data.

My motivation to start this project was that I have wanted to explore DNA data in order to to learn and maybe invent some compression algorithms for DNA data for about two decades.

Install

Install serpent with pip install serpent, or develop with pdm.

Tools provided

Work with FASTA files and sequences

• serpent cat: concatenate and print FASTA files
• serpent find: find FASTA files in directories
• serpent find -s: find and print FASTA sequences in files and directories

Convert data

• serpent encode: Convert data into different encoded representations
• serpent decode: Map codons into numbers 0...64

Analyse and plot FASTA data visually

• serpent ac: print and plot autocorrelation on DNA and RNA sequences
• serpent fft: plot FFTs on DNA and RNA sequences
• serpent hist: plot histogram statistics
• serpent image: visualise DNA and RNA data as images
• serpent seq: plot sequence count statistics

Statistics

• serpent codons: Print codon statistics
• serpent pep: Print peptide statistics

See serpent -h for all subcommands and serpent <subcommand> -h for options!

Sample data

Get some sample data from NCBI datasets – I recommend starting with virus, bacteria or archea genomic data as they are smaller than plants or animals.

• National Center for Biotechnology Information
• Datasets - NCBI - NLM
• RefSeq: NCBI Reference Sequence Database
• Home - Nucleotide - NCBI
• Home - Protein - NCBI
• Genome - NCBI - NLM

A SARS-CoV-2 genome is only 29 kb for example!