Global Alignment tool

Question

[Khaled]

I'm making an alignment tool so that is the global method. I wanted to know if the result of my tool was correct so I compared it with NCBI the results are pretty similar and I want to know if that is good and if there is another way to check my results?. secondly, the process takes so much time to proceed with the results, it took 10:15 minutes at first but now it takes 2:1.30 minutes using PYPY, why pypy because it's the only method that worked well unlike numpy, numba, multiprocessing, myby, and cython and I want to know if there is another way to enhance my code speed?.

[Joe]

This isn't a very meaningful comparison because BLAST is a local aligner (it's what the L stands for), not global.

Answer 1

[Mensur Dlakic]

People often say to others that they are reinventing the wheel, but rarely has that been so true as in your case. There are excellent tools for global alignment, and it is unlikely that you can develop a better tool, especially in python. I say this without any intention to insult you - odds are against you as this area of research has been active for at least half a century.

Instead, I suggest you Google global nucleotide alignment and follow the many links that will be available. I will get you started.

• https://embossgui.sourceforge.net/demo/manual/needle.html
• https://www.ebi.ac.uk/jdispatcher/psa/emboss_needle
• https://fasta.bioch.virginia.edu/fasta_www2/fasta_list2.shtml