Help - Quick Start

PhylomeDB User's Manual Index

Quick start

Phylomes are the complete collection of phylogenetic trees derived from a completely sequenced genome. In order to reconstruct them an automatic pipeline was designed that mimicked a tree reconstruction process. For detailed information about the pipeline used in phylomeDB check the pipeline information page here. Each phylome is formed by a seed proteome, which is the starting point of phylome reconstruction, and a group of proteomes against which the seed is queried.

PhylomeDB has been designed in order to store all the data generated during a phylome reconstruction. Information about phylogenetic trees, alignments and orthology predictions can be found stored in the database.

You can see a 4-minutes introductory tutorial here (thanks to OpenHelix Blog).

 

Starting Page

The image below shows the main page of phylomeDB and indicates the most important features so you can quickly start using phylomeDB.

 

a) Search engine: This option allows for the search of an entry using a protein code. Codes that work in PhylomeDB include the internal Phylome ID, Ensembl, SwissProt, SwissProt TrEMBL or NCBI NonRedudant IDs. A left click on the Search button will perform the search and retrieve the entry/entries that match the query. Random trees can also be visualized by pressing on the Random Tree! link. Additionally, pressing on the "Blast search" link will open a box in which a protein sequence can be introduced and a standard Blast search will be executed.

b) Latest phylomes: This shows the last phylomes that have been made public in phylomeDB.

c) PhylomeDB uses: PhylomeDB relies on some external tools, the icons found in this part of the starting page link to the main pages of the tools.

d) Content browser: Using these links you can access other parts of phylomeDB:

  • Collections: As the number of phylomes stored in phylomeDB grows, browsing through them to find the one you're looking for may become more onerous. Collections group phylomes that have a common subset of species to facilitate browsing. Collections can be linked to groups of related species or to a given project.
  • Phylomes: This will link you to the complete list of publicly available phylomes.
  • Downloads: Leads to a ftp page where all the information regarding the phylomes can be downloaded. Downloads from single trees or alignments can be done directly from the tree page.
  • Help: leads to this manual.
  • FAQ: Frequently asked questions.
  • About: Information about how to cite phylomeDB and about the people involved in mantaining the database.

e) Latest story involving phylomeDB

f) Popular phylome collections: List of collections that are more often accessed by phylomeDB users.

g) Latest news: List of collections that are more often accessed by phylomeDB users.

h) Databases that cross-link to phylomeDB: List of databases that cross-link to phylomeDB.

 

Tree interface

The primary entry page accessed after a search will show the phylogenetic tree for the searched protein that was most recently reconstructed. As seen in the image, the page can offer different kinds of information.

 

 

a) Tree search panel : allows switching among all available trees containing the target sequence, even if it was not used as a seed (i.e. collateral tree).

b) Tree editing menu: allows to search nodes matching custrom criteria, select what tree features are shown in the image and download image or other data.

c) Lowly supported nodes are highlighted with a transparent bubble and speciation and duplication events are indicated using red and blue colors, respectively.

d) A taxonomy panel indicating the assignment of different partitions to major taxonomic levels. Taxonomic level associated to each color is shown on mouse over events.

e) Domain and sequence panel. PFAM motifs are represented by different shapes and can be clicked for extended information. Inter-domain coding regions are shown using the standard amino acid color codes. Gap regions are illustrated as a flat line.

f) Available tree features. One or more attributes are allowed to be selected to modify the default aspect of the tree image.

g) The tree legend indicating color codes of the different tree nodes.

h) The search panel allows to search for node matching any custom criteria of a number of node attributes. In the example shown, a node containing the P53_C domain has been highlighted through the use of this panel.

i) The contextual node menu, including extended information about a node and links to external data source.