DiAlign
Introduction
DiAlign is a (DNA or protein) alignment program that relies on comparison of whole segments of sequences instead of comparison of single nucleic/amino acids.
DiAlign constructs alignments from gapfree pairs of similar segments of the sequences. Such segment pairs are referred to as diagonals.
Every possible diagonal is given a so-called weight reflecting the degree of similarity among the two segments involved. The overall score of an alignment is then defined as the sum of weights of the diagonals it consists of and the program finds an alignment with a maximum score - in other words: the programme tries to find a consistent collection of diagonals with a maximum sum of weights.
DiAlign does not use any gap penalty, thus avoiding this critical parameter. Consequently the program is especially suited to detect local similarities in otherwise completely unrelated sequences.
In the example below, the sequence segments corresponding to diagonals are underlined in each sequence. The color corresponds to the segment of the other sequence involved in the same diagonal. Lower case letters indicate amino acids that are not included in any diagonal and remained unaligned. The first diagonal shown in the alignment consists of the TPLPSH segment of HTLV_II and the APLPIH segment of HBV. The rows of * signs below the alignment symbolise the degree of overlapping diagonals at each point.
DiAlign is free of charge and is accessible at http://www.genomatix.de/cgi-bin/dialign/dialign.pl