Task_Jan_20

A small exercise to get familiar with how sequences and alignments are stored / represented

align_seq.sh Script Overview

• Align sequences by passing the a fasta file to be aligned as the first argument
• The program will ask the user to choose between fasta and clustal format
• A file is created for the aligned sequence in their format of choice
• The file will be have the same base name as their input file
• _aln.fasta will be appended if they requested fasta format
• .aln will be appended if they requested clustal format

Demo Files

• Three sequence files appear in the repository:

1. FOXP2.fasta A file of sequences downloaded from the NCBI
2. FOXP2_aln.fasta The output of running "align.seq.sh FOXP2" and not opting for clustal format
3. FOXP2.aln The output of running "align.seq.sh FOXP2" and opting for clustal format

Storage of Fasta and clustal files

1. Fasta
   • Starts with a header line which always begins with > followed by an identifier
   • Then the sequence
2. Clustal
   • Header line which describes the alignment
   • An identifier at the beginning of each line, and the aligned sequences on the right
   • Each column represents the same position in all of the sequences
   • The --- represents missing data in those positons of a sequence
   • The goal is to identify conserved regions and variable regions

Setup Instructions

1. Python environment setup and installing dependencies

To keep dependencies isolated, create a virtual environment:

# Create a virtual environment in the .venv folder
python -m venv .venv

# activate the virtual environment
source .venv/bin/activate

# Install a package when you are in the virtual env
pip install -r requirements.txt

# deactivate it
deactivate

2. MAFFT Installation

MAFFT is required to use the sequence alignment tools in this project. You can install MAFFT on macOS via Homebrew:

# Install Homebrew if not already installed
/bin/bash -c "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/HEAD/install.sh)"

# Install MAFFT
brew install mafft

How MAFFT Aligns Circularly Permutated Sequences

The following example demonstrates how MAFFT fails to produce the best alignment of circularly permutated sequences

Input

> seq1
ACGTAAATTAAA
> seq2
AAACGTAAATTA

Output:

seq1            --acgtaaattaaa
seq2            aaacgtaaatta--
                  **********