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User manual

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Sebastian Wilzbach edited this page Jun 3, 2016 · 12 revisions

Input Data:

Data files can be provided to the MSAViewer in the following formats:

  1. MSA in FASTA or CLUSTAL formats. Example file in CLUSTAL format.
  2. Sequence annotation in GFFv3 or JalView format. Example file in GFFv3 format.
  3. Phylogenetic tree in Newick format. Example file in Newick format.

Once the MSA file is uploaded, the alignment can be visualized in two panels: the main panel and the overview (bird’s eye view) panel.

User’s control:

Import

Allows input file upload from an URL, disc drive or by drag & drop

Sorting

Alignment sorting by unique sequence identifiers, by sequence labels, sequences, sequence identity to the consensus sequence (calculated on the fly and is built of most frequent bases at each position of the alignment), and/or by the percentage of gaps. Also once the consensus sequence is calculated (triggered through the ‘Extras’ button -> ‘add consensus seq’), it can be put on top of the alignment

Filter

Hide sequences and/or columns by a certain percent of sequence identity, by certain percentage of gaps or by selection

Selection

Search an alignment for a motif using a regular expression (e.g. K(K|R)RK for a nuclear localization signal) or invert the selection of columns and/or rows

Vis. elements

Show or hide the overview panel, the sequence logo representation of the alignment, meta information (i.e. the percentage of gaps and the sequence identity to the consensus sequence), a histogram representation of gaps and/or of amino acid conservation at each column in the alignment. Furthermore, column numbers, sequence counts and sequence labels can be shown/hidden from the visualization. You can use your ctrlKey or metaKey to select multiple residues, columns or sequences.

Color scheme

Choose one of the 15 pre-defined color schemes or select to use none

Extras

Allows adding the consensus sequence (composed of most frequent bases at each position in the alignment), increasing or decreasing the font size, or navigating to a certain column number through clicking on “jump to a column”

Export

Export the URL of the visualization for e.g. embedding it in your own website or as a high quality image. Exported can also be the entire alignment, selected sequences (both in FASTA format), or annotation features (in GFF format). Furthermore, the alignment can be viewed in JalView, which is launched automatically.

Integration with the phylogenetic tree:

Once the MSA and the corresponding phylogenetic tree files are loaded, sequences in the alignment and branches in the tree get synchronized such that:

  • Selection of a sequence in the alignment highlights a leaf corresponding to this sequence in the tree and vice versa
  • Collapsing a branch in the tree and thus making the leaves of this brunch invisible hides the sequences corresponding to these leaves in the alignment
  • Conversely, uncollapsing a branch in tree and thus making the leaves of this branch visible again, makes the sequences corresponding to these leaves visible in the alignment as well

These functionalities can easily be tested on our tree demo site.

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