Blast Parameters (reward/penality) (gapopen/gapextend)

[mido1951]

Hello,
i posted this message in other website but i haven't responses.

I want to set parameters for Blastn (reward / penalty- gap / gapextend).
I read on the blast site:

"It is important to choose reward/penalty values appropriate to the sequences being aligned with the (absolute) reward/penalty ratio increasing for more divergent sequences. A ratio of 0.33 (1/-3) is appropriate for sequences that are about 99% conserved; a ratio of 0.5 (1/-2) is best for sequences that are 95% conserved; a ratio of about one (1/-1) is best for sequences that are 75% conserved"

I want to know what that means "99% conserved" and "95% conserved" and "75% conserved"?

and if reward>penalty, how can one say of these sequences?

because in the table there are:

r/p gap/gapext
3/-2 5/5
5/-4 10/6, 8/6

[mido1951]

any responses?

[mastal]

'% conserved' means percent similarity of the sequences.

Blast looks for sequences that are evolutionarily related, so 'conserved'.

[mido1951]

thankyou.
for the evalue.
do it's best to minimize the value E-value? for example 1e-35?
or is it the opposite?

[GenoMax]

What do you think (http://blast.ncbi.nlm.nih.gov/Blast....E=FAQ#expect)?