Match -> Align

Match -> Align creates a sequence alignment based on the alignment of structures in Chimera. Residue types are not used, only their spatial proximities. For an informal introduction, see the Alignments tutorial. See also:

Meng, E.C., Pettersen, E.F., Couch, G.S., Huang, C.C., and Ferrin, T.E. "Tools for integrated sequence-structure analysis with UCSF Chimera." BMC Bioinformatics 7(1):339 (2006).

There are several ways to start Match -> Align, a tool in the Structure Comparison category.

Chains to be included in the sequence alignment should be chosen from the top part of the panel. The Residue-residue distance cutoff (angstroms) determines which residues can potentially be aligned in the output sequence alignment (default 5.0). Distances are measured between the CA atoms of amino acid residues and the C4' atoms of nucleic acid residues. The Gap character can be a period (.), dash (-), or tilde (~).

The method used to construct the sequence alignment depends on whether the alignment is pairwise (two chains chosen) or multiple (more than two chains chosen). The resulting sequence alignment is opened in Multalign Viewer.

PAIRWISE ALIGNMENT

In the pairwise case, a modified Needleman-Wunsch procedure (dynamic programming) is used to determine the sequence alignment that best represents the structural alignment; the score for aligning a pair of residues is:

(cutoff – distance) for distances no greater than the cutoff
–1 for distances greater than the cutoff

The gap penalty is zero, since for this application the spatial proximity should be more important than adjacency in sequence (residues farther apart than the distance cutoff should not be aligned). The Needleman-Wunsch procedure enforces the directionality of the chains, however, which is why it is necessary to double one sequence to Allow for circular permutation. The number of residue pairs aligned is reported in the status line and Reply Log.

MULTIPLE ALIGNMENT

In the multiple case, a different, semi-heuristic algorithm is applied. There are two ways in which the cutoff can be applied to constructing the multiple sequence alignment, Residue aligned in column if within cutoff of:

at least one other
all others (default)

(in the pairwise case, these conditions are identical). Allow for circular permutation permits sequences to be doubled as needed; information on any permutations found is sent to the Reply Log.

UCSF Computer Graphics Laboratory / July 2006