Multiple Sequence Alignment

Accessing the Multiple Sequence Alignment Viewer on the PATRIC Website

This tool may be accessed from the “ MSA” Tools button in the light blue Table Toolbar at the top of PATRIC tables, including the Table Toolbar within your Workspace.  From within the Protein Family Sorter you may chose to access MSA via the Table Toolbar or to conduct MSA for ALL protein members on any FIGfam details page by clicking “For All XX Members” link under “Integrated Protein Tree and Alignmentin the upper right corner of the page.  For more details on the Protein Family Sorter please see Protein Family Sorter FAQs.

Multiple Sequence Alignment Viewer Overview

The multiple sequence alignment viewer is an interactive tool that displays multiple sequence alignment and a family tree side-by-side and allows the user to examine details of selected protein families, including the overall quality of the alignment as well as more specific details such as particular regions or motifs of interest.

Alignment Program and Source Data

The protein sequences from each family are aligned using MUSCLE (v 3.6) and
ambiguous portions of the alignment are removed using Gblocks (v 0.91b).  The input data for the multiple sequence alignments are the protein sequences that have been grouped together in a FIGfam.  When the user selects a FIGfam from the protein family sorter, all members of that FIGfam from the set of genomes being examined are included.

Multiple Sequence Alignment Viewer Features and Functionality

  • The Family Tree, displayed on the left side of the screen, may be collapsed or expanded in order to co-locate sequences of interest.
  • A scroll bar, located at the bottom of the alignment, allows for visualization of specific regions throughout the amino acid sequences.
  • The Family Tree display can be switched between phylogram and cladogram views.  In phylogram view, the tree branches are drawn with lengths based upon the branch lengths in the tree.  In cladogram view, the tree branch lengths are disregarded and branches are drawn so all branch labels line up on the right side of the Family Tree.  Phylogram view conveys additional information about the evolutionary divergence, while the cladogram view allows better visual resolution of the branching pattern for very closely related taxa (where the branch lengths are too small to allow the branching pattern to be distinguished in phylogram view).   Cladogram view also shows branch support values, which are calculated by FastTree.
  • You may chose to label the Family Tree with locus tags or genome names.  In either view, you may momentarily see both the locus tag and genome name identifiers by placing your mouse over a specific branch label in the tree.
  • Within the alignment, columns highlighted in black are considered conserved.  You may adjust the conservation sensitivity with the slidebar located at the top of the alignment.
  • Clicking within the alignment will highlight the selected amino acid column in blue and show the numerical position designator for that column along the top of the alignment.  It will also automatically highlight the coinciding genome branches in the Family Tree with the same colors as their respective amino acids in the alignment.
  • Both the alignment and the Family Tree are printable by clicking on “Printable Alignment” and “Prinatble Tree” respectively at that top of the table.  Note:  The Family Tree may be printed in either phylogram or cladogram view.