alignerviz - Visualize many sequences in three dimensions.
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