I have a sequence belonging to a protein, when I submitted using Megablast option but it never matches with homologous proteins. However, using Blastn option it matches with the proteins I am dealing with. It seems some shifts in the sequence might be visible using blastn. What should I do for my sequence after this point?
K. Sonal Choudhary
Megablast is for highly similar sequences, blastn matches even with less similarity. You should check the result of blastn, may be the identity or query coverage is very low and its matching just by chance. For accuracy, identity should be 30% and query coverage should be more than 65-70%. You can check by blastx too.
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