Entering edit mode
2.8 years ago
ashenafymamo
•
0
I tried to align two nucleotide sequences using NCBI "blast" with "Align two or more sequences" program and Mega 6 software . The results of the two alignment programs are different. The NCBI alignment starts at 57 nucleotides whereas using Mega 6 software, it starts at nucleotide one.
Is there any explanation for this?
Without knowing the details of what the two sequences are and how they are related to each other I will speculate that BLAST prioritized local alignment over a global when compared the one that MEGA did. Difference could also be various parameters you can choose with either programs. If the sequences are related (and are of similar lengths) than you may be able to get one to do what the other is doing by changing alignment (e.g. penalties) parameters.
Dear GenoMax Thank you for your prompt response.
Both the sequences are a whole-genome Sapelovirus sequence (highly similar). I have tried running NCBI's blastn and megablast programs by changing "word size" and "Match/Mismatch Scores" parameters and gave me the same result, which is different from mega software.
Could this difference come from differences in the local alignment nature of NCBI's BLAST and Mega's global alignment algorithm? or what would be the other possible reasons?
Thanks