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 <[EMAIL PROTECTED]> 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 > > > --------------------------------- > Abra sua conta no Yahoo! Mail, o único sem limite de espaço para > armazenamento! > _______________________________________________ > BBB mailing list > [email protected] > http://www.bioinformatics.org/mailman/listinfo/bbb > _______________________________________________ BBB mailing list [email protected] http://www.bioinformatics.org/mailman/listinfo/bbb
