Editing Sequence alignment (section)

===DALI===
The DALI method, or [[distance matrix]] alignment, is a fragment-based method for constructing structural alignments based on contact similarity patterns between successive hexapeptides in the query sequences.<ref name=holm>{{cite journal | journal=Science | volume=273 | pages=595–603 | year=1996  |author1=Holm L |author2=Sander C | title=Mapping the protein universe | pmid=8662544 | doi = 10.1126/science.273.5275.595 | issue=5275 | bibcode=1996Sci...273..595H | s2cid=7509134 }}</ref> It can generate pairwise or multiple alignments and identify a query sequence's structural neighbors in the [[Protein Data Bank]] (PDB). It has been used to construct the [[Families of structurally similar proteins|FSSP]] structural alignment database (Fold classification based on Structure-Structure alignment of Proteins, or Families of Structurally Similar Proteins). A DALI webserver can be accessed at [https://web.archive.org/web/20090301064750/http://ekhidna.biocenter.helsinki.fi/dali_server/start  DALI] and the FSSP is located at [https://web.archive.org/web/20051125045348/http://ekhidna.biocenter.helsinki.fi/dali/start The Dali Database].