Difference between blastp and phi-blast
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5.2 years ago

Dear all, I came across some questions concerning blastp and phi-blast.

We all know that phi-blast use pattern-initiating way to search for the seed region and then score the flanking region to give the score of sequence in database. That's why that the hits in phi-blast in normally less than hits in blastp result, since the pattern set quite a restriction on the sequence while the seed words in normal blastp search can vary.

However, when I run the phi-blast without a pattern(leave the pattern blank), I got more hits than the blastp. Dose anyone get a hint of what is happening?

Thanks a lot for your help!!!

genome • 5.5k views
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