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Raw Alignment Score Calculation

Thanks for lots of answers and I've started with lots of sources here. It helps me to get a good introduction to blast.

After I've now a little more understanding I can ask more specific questions such as the following:

The following blast result:

ATTTGCAGAATTTGCAAAAAAATGTTTGT
|||||||||||||||    ||||||||||
ATTTGCAGAATTTGC----AAATGTTTGT

I'd like to calculate the raw alignment score: (Scoring scheme: match=1, mismatch= -2, opening gap= 3, extented gap=2)

We have 25 matches and 4 gaps. S = 25-9 = 16 or do I need to say: there are 4 gaps which are 4 mismatches and therefore we get the following raw score: S = 25-9-8= 8

Which one is correct?

Thanks! Beeth.


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