Question: Raw Alignment Score Calculation
2
Beeth170 wrote:

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.

scoring blast • 8.8k views
written 9.3 years ago by Beeth170
6
Gww2.7k wrote:

In your scoring scheme you are using an affine gap penalty. Therefore your score should be:

``````25 - ([opening penalty] + [gap extension] * (l - 1)) = 25 - (3 + 2 * 3) = 16
``````

Where `l` is the length of the gap. The mismatch score is only used when the aligned bases mismatch outside of a gap.