Sequence Alignment with NW Algorithm

Summary:

Implementation of Needleman–Wunsch algorithm. Compare sequences (in fasta files) and list max scored sequences. Multithreaded with OpenMP.

How To Run:

• gcc SequenceAlignment.c -o seqAlign -fopenmp
• ./seqAlign

Notes:

• Increase the LIMIT value (constant) of the program will increase the working time.
• You may need to edit THREAD value (constant) for your processor/operation system.

Approximately Execution Time:

• 1K Sequences ~ 1 min 30 secs
• 5K Sequences ~ 40 mins 30 secs
• 10K Sequences ~ 2 hours 45 mins
• 15K Sequences ~ 6 hours 15 mins

Tested on Ubuntu 18.04 with Intel i7 4710HQ processor.

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Alperen Cubuk