Tree
Sets of Reference Sequences representing bacterial and archaeal sequences were separately aligned using a secondary structure covariance model
and INFERNAL version 1.0. A maximum likelihood tree was constructed using raxmlHPC v 7.2.2 and a secondary structure file for
Thermus thermophilus 16S rRNA. Sequences used in tree construction are the same as those in the BLAST database.
The tree is arbitrarily rooted for visualization and the graphical view is similar to that developed for the NCBI Influenza project.
Search results are visualized as color-coded boxes representing the top ten hits (see above) and the entire branch where the top ten
hits appear is drawn with a shaded blue background.
The number of sequences in each branch is represented both by the size of the gray circle, and by the first number in each row. The total
number of sequences with the same taxonomic assignment is shown next, and if there are any sequences that do not share a common parent with
the majority at up to two nodes in the taxonomic hierarchy, then the total number of sequences is noted as 'other'. Yellow highlights are
used to aid in subtree visualization.
The buttons to the left and the resolution controller change how the tree is visualized or
take one to different tools. The buttons (marked with an asterisk) and additional controls and functionalities
are listed below:
Additionally there is a resolution controller for controlling the number of leaves resolved
in the tree.
Select subtree
This button selects the subtree containing the top ten hits.
Table
The table button displays full BLAST results.
Search
The search button displays a pop-up window where metadata for the set of Reference Sequences
can be searched in a field-specific manner: organism (including taxonomic lineage), strain, culture collection, minimum length, maximum length, and accession.
Successful search results are tagged by gray boxes drawn on the tree with the number in the box corresponding to the total search results in the row/branch.
Existing tags can be removed, and the form cleared for a new search term.
Reset
The reset button rests the tree to the way that it appeared after the initial search.
This will reset any rearrangements, resolution changes, and tagging. It does not reset the form
for another search. To start over with a new search the title is linked back to the original submission form.
Unselect
The unselect button removes any branch selections in the tree.
Align
The align button aligns the query sequence against the top ten hits and displays the
resulting alignment in a multiple alignment viewer that is similar to that for the SARS
alignment.
Resolution controller
The resolution of the number of leaves displayed is done via the resolution controller. A maximum of 500
leaves can be shown for each branch. Tree selection can either be done with the select subtree button (which selects the branch where hits
occurred) or done directly on the tree itself (click on the root of a branch). Once a selection occurs, the total number of leaves in the branch and
the number of leaves that are resolved is displayed aboved the resolution controller shown. Moving the red marker line from minimum (one) to maximum (up to 500) for
a given branch changes the resolution of the number of leaves in the selected subtree.
Accession
Clicking on a RefSeq Accession Number in the tree will open the flatfile view of that record in Entrez Nucleotide.
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