Align Chain Sequences

Align Chain Sequences generates a multiple sequence alignment (MSA) of structure chains in Chimera using a Clustal Omega or MUSCLE web service provided by the UCSF Resource for Biocomputing, Visualization, and Informatics (RBVI). The MSA web service can also be called from Multalign Viewer to realign an existing alignment. The coordinates of the structures are not used, only the sequences. By contrast, the Match -> Align tool generates an MSA using only the α-carbon proximities in a 3D superposition. See also: MatchMaker

Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG. Mol Syst Biol. 2011 Oct 11;7:539.

MUSCLE: multiple sequence alignment with high accuracy and high throughput. Edgar RC. Nucleic Acids Res. 2004 Mar 19;32(5):1792-7.

There are several ways to start Align Chain Sequences, a tool in the Sequence category.

Two or more Chains to align should be chosen from the list of structure chains currently open in Chimera. A contiguous block can be chosen by click-and-drag, or by clicking on the first (or last) line in the block and then Shift-clicking on its last (or first) line. Ctrl-click toggles the status of a single line.

• Use only selected part of chains (if any) (true/false) - whether to include only the selected parts of the chosen chains; if false, or if true but no part of a chain is selected, the entire sequence will be used, including residues missing from the coordinates but present in SEQRES records
• Alignment program (Clustal Omega/MUSCLE) - whether to use Clustal Omega (default) or MUSCLE

  If Clustal Omega [see the README file at the Clustal Omega website for details]:

  • Number of guide-tree/HMM iterations (1) - how many combined guide tree/HMM iterations to perform after the initial alignment; can be 0 [--iterations]
  • Use full distance matrix during initial alignment (true/false) - whether to use the full distance matrix for guide-tree calculation during the initial alignment [--full]
  • Use full distance matrix during alignment iteration (true/false) - whether to use the full distance matrix for guide-tree calculation during iteration, if any [--full-iter]

  If MUSCLE [see the command-line reference at the MUSCLE website and BMC Bioinformatics 5:113 (2004) for details]:

  • Maximum number of iterations (16) - maximum number of iterations [-maxiters]
  • Maximum time to iterate in hours (0 means no limit) (0.0) - maximum run time [-maxhours]
  • Find diagonals (faster execution if sequences are similar) (true/false) - whether to use segments of high sequence similarity to constrain the alignment; may improve speed but at the expense of some accuracy [-diags]

OK initiates the calculation and dismisses the dialog, whereas Apply initiates the calculation without dismissing the dialog. The job will be run in the background; clicking the information icon in the Chimera status line will bring up the Task Panel, in which the job can be canceled if desired. Cancel dismisses the dialog, and Help opens this manual page in a browser window.

The output sequence alignment will be opened automatically in Multalign Viewer.