Blastn: In The Scoring Parameters, What Does "Linear" Mean?

The title says everything: I someone able to explain to me, what the "linear" option in section "scoring parameters" does mean?

I understand the Existence/Extension costs, just not the "linear" option...

blastn alignment

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updated 5.4 years ago by Biostar

• written 12.4 years ago by mschmid

1 answer

I believe that it means that the the score is is a linear function of the attribute that gets measured.

Other way to say that is linearly proportional: for example twice as long gaps will lead to twice as large penalty.

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written 12.4 years ago by Istvan Albert

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