alenzhao / smith-watermanalgorithm

algorithm for finding local sequence alignments

Smith-WatermanAlgorithm

algorithm for finding local sequence alignments

Example use

from command line:

navigate to the src folder.

pass the FASTA files as arguments.

python align.py seq1 seq2 

Example output

Results are saved to the results file.

GCTACGACTCAGCTCAGTGAGCTGCATGCCTTCAAGCTTCGGGTGGAT-CCTGCCAACTT
 |  | | |      ||    |    | ||  | | |      | |     |  |     
-CGCC-AATTTCA--AGAT-TC-T-GT-CCCAC-AACA--TCCTCGTGG--T-TCTGG-C

TAAGATC-CT--GGC-CCACAACATGATGTTGGTAATCGCCATGTACTTCCCTGGCGAGT
 |   |   |    |    |   |         |   |  |   |        |||    
CACTTTGT-TCCC-CG---CCG-AC--------TTCACT-C--CTG---A---GGCTCA-

TCACTCCAGAGGTCCACCTCTCAGTTG-ACAAGTTCCTTGCGTGCCTGGCTTTGGCTCTG
|   | |        |     ||  |   |    | | |  |   |||||| ||||  ||
TG-TTGC-----A--ATGGA-CAAGT-TCC----T-C-TCAGCT-CTGGCTCTGGCCATG

TCTGAGAAGTACCGCTAAA
|||||||||||| | ||||
TCTGAGAAGTACAGATAAA

Score: 142