Space, not running time, is often the factor limiting the application of dynamic programming. Often cubic space is required to align three sequences (3D dynamic programming). Given this space requirement, alignment of three genes with a length of more than 1000 characters is almost infeasible in most of our modern computers. Here, by using a divide conque technique, I implemented alignment of three sequences in quadratic space. The idea of this implementation is similar to Hirschberg's algorithm, which I have an implmentation in Python, see here.
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Python version >2.7
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package: [numpy] (http://www.numpy.org/)
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package: [Biopython] (http://biopython.org/wiki/Main_Page)
Below command will write the alignment of three sequences stored in file test1, test2 and test3, respectively to a file named with test1_test2_test3 to the current directory. In addition to the alignment, the file also contains the memory and time usage information.
python alignmentThreeSeq.py test1 test2 test3
To display help
python AlignTwoStringInLinearSpace.py -h
Zhigang Wu (zhigang.wu@email.ucr.edu)
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