A simple tool to visualize sequences using Vlachos et al's technique
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README.md
aviz.py
example.png
test.fasta

README.md

alignerviz - Visualize many sequences in three dimensions.

Example of alignerviz's ouput

About

Large genomic sequences are often difficult for the human eye to visualize. In the paper Visual Exploration of Genomic Data, Michail Vlachos, Bahar Taneri, Eamonn Keogh, and Philip S. Yu (2007) suggest converting sequences to trajectories. Each nucleotide is a vector, based on:

A = (0, 1)
T = (1, 0)
C = (0, -1)
G = (-1, 0)

and these vectors are connected beginning to end from an initial starting point. A large sequence difference will quickly push a trajectory in a different direction, while more similar sequences will have similar trajectories.

Requirements

  • Python (>= 2.5)
  • matplotlib
  • numpy

Usage

Run alignerviz with:

python aviz.py sequences.fasta

If there is a specific FASTA entry that needs to be highlighted, specify with its header:

python aviz.py -H seq_header_name sequences.fasta

Specific graphic options can be set too. For example, if there are many very similar sequences it may be useful to specify an alpha, and print each one in black:

python aviz.py -b -a 0.4 sequences.fasta

Line width can also be specified:

python aviz.py -l 3 sequences.fastq