The tree shows the occurrence of this domain across different species.
More...
Species trees
We show the species tree in one of two ways. For smaller trees we try
to show an interactive representation, which allows you to select
specific nodes in the tree and view them as an alignment or as a set
of Pfam domain graphics.
Unfortunately we have found that there are problems viewing the
interactive tree when the it becomes larger than a certain limit.
Furthermore, we have found that Internet Explorer can become
unresponsive when viewing some trees, regardless of their size.
We therefore show a text representation of the species tree when the
size is above a certain limit or if you are using Internet Explorer
to view the site.
If you are using IE you can still load the interactive tree by
clicking the "Generate interactive tree" button, but please
be aware of the potential problems that the interactive species tree
can cause.
Interactive tree
For all of the domain matches in a full alignment, we count the
number that are found on all sequences in the alignment.
This total is shown in the purple box.
We also count the number of unique sequences on which each domain is
found, which is shown in green.
Note that a domain may appear multiple times on the
same sequence, leading to the difference between these two numbers.
Finally, we group sequences from the same organism according to the
NCBI
code that is assigned by
UniProt,
allowing us to count the number of distinct sequences on which the
domain is found. This value is shown in the
pink boxes.
We use the NCBI species tree to group organisms according to their
taxonomy and this forms the structure of the displayed tree.
Note that in some cases the trees are too large (have
too many nodes) to allow us to build an interactive tree, but in most
cases you can still view the tree in a plain text, non-interactive
representation. Those species which are represented in the seed
alignment for this domain are
highlighted.
You can use the tree controls to manipulate how the interactive tree
is displayed:
- show/hide the summary boxes
- highlight species that are represented in the seed alignment
- expand/collapse the tree or expand it to a given depth
- select a sub-tree or a set of species within the tree and view
them graphically or as an alignment
- save a plain text representation of the tree
