FASTA sequence aligner.

pip install sequence_aligner==0.0.2




Aligner is a tool for FASTA DNA sequence alignment.

How to use

Aligner is fairly simple to use. All you need is a standard FASTA text file (*.txt).

By the way, included in this package are two example files (fasta_example_1 .txt, fasta_example_2.txt).

In order to install,

pip install sequence_aligner

To use aligner from the command line, you run the following commands:

aligner [-h] --file_path FILE_PATH [--storage_path STORAGE_PATH] [--results_name

FILE PATH is the path to the fasta sequence text file.

While FILE PATH is required, STORAGE_PATH and FILE_NAME are optional.

By default, the result file will be stored in the following generated directory: /tmp/sequence_results

And the file name will be generated with the following pattern: sequence_read-<datetime here>.txt for example: sequence_read-2016-07-01T16.42.21.246183.txt

Once you run the command line, within seconds, your results will be generated, and you'll receive a print out of the location and name of your file.

For example: Sequence Alignment results stored --> /tmp/sequence_results/sequence_read-2016-07-01T17.59.48.458859.txt

How it works

In order to align sequences, first, I created a dictionary of all subsequences from the size 'greater than half' to full length.

One sequence in the list of sequences was designated the "anchor sequence".

I gathered that at any given state of the anchor sequence, there would exist a sequence with the the greatest overlap. Iterating through the sequence list, the sequence with the sub-sequence (from the dictionary mentioned above) having the greatest 'score' is identified. The score is based on the amount of overlap with the anchor sequence. This subsequence is then merged into the anchor sequence. This iteration continues until all sequences in the sequence list have been merged into the anchor sequence.


  • One issue I dealt with was speed. After many iterations of refactoring, I was able to bring runtime down from ~45-50 min to ~10-11 min.
  • This program assumes that sequences overlap and that there are no mutations.

Next Steps

  • Improve efficiency
  • Improve 'match-iness' algorithm -- right now, my 'score' is merely based on length of overlap at a given state of the anchor sequence. More preprocessing could be done before commencing alignment in order to score the level of 'matchiness' between all pairs of sequences.