Implementation of Hirschberg's algorithm; linear space implementation of dynamic programming
The factor limits dynamic programing's application often is not running time (O(nm)) but the quardratic space requirement, where n and m are the length of two sequence. The Hirschberg algorithm reduces the space requirement from O(nm) to O(n) by involves divide and conque technique in the dynamic Programming process. Below is an implementation of Hirschberg's algorithm.
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Python version >2.7
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package: [numpy] (http://www.numpy.org/)
To display help
python AlignTwoStringInLinearSpace.py -h
Below command will write the alignment of two sequences to the STDOUT
$ python AlignTwoStringInLinearSpace.py file1 file2
######## Alignment 0 ########
ATGG
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ATCGZhigang Wu (zhigang.wu@email.ucr.edu)
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