/sequence-alignment-with-nw-algorithm

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

Primary LanguageC

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.

Alperen Cubuk