PhylomeDB Guide

This guide is intended as a source of reference for those participating in the “Climb up the Tree” pilot program, and also as a document for anyone interested in how this powerful tool works.

Home Page
Search
Navigation Tabs

Results Page
Interactivity
Tree Search
Tools and Downloads Menu
Taxonomy Markers
Protein Domains
Node Legend
Orthology Prediction

Home Page

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The home page includes different elements.

We will focus on the following:

(a) Search Engine. Type the name or code of the protein of interest in this box. Click on the Search button to perform the search. Go to the corresponding section in this guide.

(d) Navigation Tabs. The Help tab is particularly interesting, as it provides further information that goes beyond the scope of this guide. Go to the corresponding section in this guide.

You can find more detailed information about these elements in the tool’s help page.


Search

You can search proteins by their name. If you wish to narrow your search, you can also search proteins by their code. The search engine recognizes several code formats.

The tool looks for the specified protein. If no tree has been reconstructed from this protein, you will be shown the tree of the closest homolog included in the protein.

If you do not obtain the desired results after searching by name or ID, you can also search by BLAST. This allows you to search from a specific amino acid sequence. This search retrieves a list of proteins similar to the sequence you have provided. From this list you can access the different trees.


Navigation Tabs



Results Page

Just like the home page, this page includes several areas with information. The most relevant areas are:

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  1. Tree Search Panel
  2. Downloads and ToolsMenu
  3. Relationship Tree. In (g) we find the node legend.
  4. Representation of the different domains of the proteins.
  5. List of tree features that can be added to trees.
  6. Node Legend

Click on the link below the tree to obtain orthology predictions through metaPhOrs.

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As previously mentioned, you will find more detailed information in the tool’s help page.


Interactivity

All the elements in a tree are clickable. Clicking on an element expands a contextual drop-down menu containing information related to that particular element.

For example, when you click on a branch, you can hide its sons, change their order, establish the branch as a root, etc.


Tree Search

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The first drop-down menu allows you to switch between trees built from the protein of interest. An empty drop-down menu indicates that the species of the protein searched has never been used as a base to build a phylome.

The second drop-down menu allows you to switch between the evolutionary models used to build de phylome. Seven different models are tested, and the ones which retrieve the most mathematically favorable results are displayed in the drop-down menu.

The third drop-down menu shows trees which include the protein of interest but are not built from it. These are called collateral trees.

You can find technical information on how to use the tool in its help page.

Tools and Downloads Menu

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  • Tree Features. Opens up a menu to show/hide different information on the proteins in the tree. You can click on Refresh to update the tree with the selected changes.
  • Search. Opens up the search menu that allows you to search for information within the tree. The branches found under the search criteria will be marked with a yellow bubble.
  • Clear Search. Clears the searches made within the tree.
  • Image (PNG o SVG). Allows you to download an image file for the tree. SVG is a vector image format.
  • Hard Link. Opens up a new tab with a permanent link to the generated tree.
  • Download OrthoXML. Opens up a new tab containing a text file in xml format with the information to represent the tree.
  • See Alignments. Opens up a new tab containing all the amino acid sequences aligned.
  • Download data.tar.gz. Downloads a compressed file with all the information of the tree.

Tree Features

Click on the image to enlarge it

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Example of an alignment of protein sequences

Click on the image to enlarge it
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Taxonomy Markers

Shows the taxonomic relationships with the species from which the phylome is built.

Each color corresponds to a level in the taxonomic hierarchy (colors may vary in each phylome).

Click on each color to obtain more information on the corresponding taxonomic level.

For example, when you build a phylome from the human TP53, you will find the taxonomic information of the image by clicking on the purple block.

As shown in the image, the colored block extends through all results sharing a specific taxonomic level, even if they aren’t adjacent.

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  • Pink: Opisthokonta
  • Red: Chordata
  • Green: Teleostomi
  • Blue: Amniota
  • Yellow: Mammalia
  • Orange: Laurasiatheria
  • Green 2: Eutheria
  • Orange 2: Primates
  • Purple: Hominidae
  • Orange 3: Tetrapoda

Protein Domains

Different protein domains are shown. These domains are represented by geometric shapes (squares, rhombuses, etc.). Each shape includes the name of the corresponding domain, although it may be shortened.

The amino acids in interdomain coding regions are shown as vertical lines, using the standard amino acid color codes.

Horizontal black lines indicate gap regions in a comparison between species. During evolution, some proteins may have “lost” or “gained” entire regions. In the P53 protein tree, for example, you can see how the Bos taurus p53 protein, which is a paralog of P53, has lost all its initial coding region. This region is still present, although with some differences, in the rest of species.

The large domains have been identified from the PFAM database.

This example shows that all proteins share the p53 domain as well as a “_tetra” domain. The first protein, which is found in the Drosophila melanogaster, shows a P53_C domain absent in the rest of proteins. Except the first three, almost all the other proteins also share a “SAM_2″ domain.

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You can click on a protein and select the TreeFam option (if available) to obtain more information on these domains.

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This option will take you to the TreeFam page for the corresponding protein. Hovering the mouse pointer over the different domains will allow you to enlarge their name and information. In the example, the “_tetra” domain corresponds to P53_tetramer.

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You can also click on the TrEMBL (uniprot) direct link to get tons of addtional information, such as the family and domains of the protein of interest (Family & Domains section).


Node Legend

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Speciation events are shown in blue. In these cases, the gene is shared by two or more species. The differences between the genes in these species are due to the different evolutionary paths followed by each one of them, not to a particular event of the gene (such as a duplication).

Duplication events are marked in red. In these events, a gene was duplicated and each copy followed a different evolutionary path.

The sequence used to build the tree is marked with a green bubble.

The low consistency of a branch according to the chosen model is marked with a pink bubble. The lower the radius, the less consistence. This indicates the node is less reliable (i.e., less likely to be correct).

Internal search results (according to the editing menu) are marked with a yellow bubble.

Go to the tool’s help page for more information on how nodes are defined.

 


Orthology Prediction

On top of relationship trees, PhylomeDB also offers a direct link to metaPhOrs, another free tool that allows you to generate predictions of the evolutionary relationships between species.

This tool carries out different comparisons based on seven services, and shows the results for each one of them. It also provides a consensus result based on the different tools. We recommend you visit the tool’s web page, <a href=”http://orthology.phylomedb.org/?q=home”>to delve into these results.

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