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
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
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