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

    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

  • #2
    any responses?

    Comment


    • #3
      '% conserved' means percent similarity of the sequences.

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

      Comment


      • #4
        thankyou.
        for the evalue.
        do it's best to minimize the value E-value? for example 1e-35?
        or is it the opposite?

        Comment


        • #5
          What do you think (http://blast.ncbi.nlm.nih.gov/Blast....E=FAQ#expect)?

          Comment

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