[BiO BB] Clustal Gap Penalties

Iain Wallace iain.m.wallace at gmail.com
Thu Mar 6 00:17:18 EST 2008


Hi,

ClustalW uses an affine gap penalty which means that it is harder to open a
gap than extending a gap. There are two parameters a gap opening penalty and
a gap extension penalty. This is discussed in more detail here
http://homepage.usask.ca/~ctl271/857/affine_gap_penalties.shtml. I think the
actual algortihm implementation is described by Gotoh (1990 PMID:2165832)
and the group to group alignment stage (moving from pairwise alignment to
groups of sequence alignment) is described by Gotoh (1994, PMID: 7804871)

It also scales these two parameters based on the substitution matrix that is
used for the alignment.
There are also a couple of methods for increasing/decreasing these scores
depending on the context of the sequence such as secondary structure or
terminal gaps, which are discussed in the help manual,
http://align.genome.jp/clustalw/clustalw_help.html

Hope this helps

Iain


On Wed, Mar 5, 2008 at 2:09 PM, Ulisses Dias <ulimard at yahoo.com.br> wrote:

> Hi all,
>
>  I'm trying to understand the clustal gap penalties that is in Thompson,
> 94, but It's very hard to do so without examples and so on. Anyone knows
> where I can find a detailed explanation about it?
>
> Best regards
>
>
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