Block-wise alignment of nucleotide sequences?

Kevin Karplus karplus at
Mon Mar 15 13:34:16 EST 2004

In article <bet550png23o07kepvr7hoarkn4el9oi38 at>, Peter Frank wrote:
> Andreas Wilm wrote:
>>What exactly do you mean by "block-wise alignment"?
> I meant local alignment.
>>Maybe Dialign is what you are looking for :
> And this program obviously does local alignments (from the website
> "Here, DIALIGN was found to be the best method for local multiple
> alignment."), so it may be suitable for my purposes. Thanks for the
> link.

Block alignment is not the same as local alignment.

The local/global distinction is orthogonal to the choice about whether
to use blocks or affine gaps.  A block aligner has a different notion
of gaps than the usual affine gap costs.  Instead of charging for gap
opening and for gap extension, the block aligners usually put a bound
on the number of contiguous blocks of aligned columns that are allowed
(that is on the number of gaps allowed), but make no distinction
between short and long gaps.  (Local vs global in a block aligner is
mainly about how end gaps are counted---I think that the default of
most block aligners is local alignment, but that is not an essential
feature of the method.)

Neither the affine gap model nor the block model is a truly accurate
reflection of evolution of sequences, but they make different sorts of
errors, so it is sometimes worthwhile to try both sorts of alignment. 

Kevin Karplus 	karplus at
life member (LAB, Adventure Cycling, American Youth Hostels)
Effective Cycling Instructor #218-ck (lapsed)
Professor of Biomolecular Engineering, University of California, Santa Cruz
Undergraduate and Graduate Director, Bioinformatics
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