align

Performs sequence alignment. The alignment can either be global or local in combination with either mutual or non-mutual.

Introduction

align is a Python module that provides a general (read: not restricted to bioinformatics) implementation of both global and local sequence alignment. The alignments can further be both mutual and non-mutual. Mutual alignment is sequence alignment where both sequences are candidates for gap insertion whilst non-mutual alignment only allows for gap insertion into the second sequence.

It is implemented in C for speed and wrapped with Cython to provide the ease of use of Python. The algorithms used are Needleman-Wunsch for global alignment and Smith-Waterman for local alignment.

align uses a symmetric numpy.ndarray as scoring matrix which needs to be of dtype numpy.int16.

It also supports iterative alignments (aligning a sequence with another sequence that already contains gaps). To use this the scoring matrix needs to be of the shape (257, 257) with the last row and column being used to score matchings of the fixed gaps and the symbols of the alphabet.

Installation

Install align with python setup.py install

Usage

>>> import numpy
>>> import align
>>> S = -numpy.ones((256, 256)) + 2 * numpy.identity(256)
>>> S = S.astype(numpy.int16)
>>> s1 = align.string_to_alignment('AATGT')
>>> s2 = align.string_to_alignment('ATGAC')
>>> (s, a1, a2) = align.align(s1, s2, -2, -2, S, local=True)
>>> print('%s\n%s\nScore: %d' % (align.alignment_to_string(a1), align.alignment_to_string(a2), s))
ATG
ATG
Score: 3

License

Distributed under the MIT license. See the LICENSE file.