There are several ways to exploit the information stored in phylomeDB depending on the needs of the user: search for one single protein, browse through a given phylome or a phylome collection or download data whether from a single tree or from a whole phylome.
The main features in phylomeDB can be found in the tree pages. You can access those pages by selecting a random tree for instance (red link at the upper-left panel) or by browsing through a phylome (see below). But normally users are looking for a given protein. PhylomeDB implements two search tools that will allow you to locate your protein of interest or if it is not in the database, the closest possible homolog.
A) Text based search: This option allows for the search of an entry using the 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. As a result the user will be led to the main tree page for the searched protein. If a given protein was not used as seed, then a list of collateral trees, meaning trees in which the protein appears but was not used as seed, will appear.
B) Blast Search: PhylomeDB also allows for searches using the Blast Search option. Clicking on the Blast search link will lead you to a new page in which a protein sequence can be introduced and a standard Blast search will be executed. The results of the blast search are parsed into a table, where the first column provides the closests homologs to your query sequence and the second columns informs about the phylome in which the protein has been used. More than one phylome can be associated to one homolog. Left clicking on the sequence code will lead to the tree page while clicking on the phylome link will lead to the main phylome page.
If you are not looking for a particular protein but just want to look through a few trees the best option is to browse a phylome. To access the phylomes that are currently publicly available on phylomeDB you can click on the "All phylomes" link found at the top of the page. This will lead you to the complete list of phylomes.
The phylomeID represents a random number given to phylomes for quick identification purposes. It is followed by the name assigned to the phylome. While phylome names could be identical, the phylomeID is unique for every phylome. When a phylome has been published, a link to the PubMed page will be added on the right of the phylome name. The three links under the download column allow the easy access to the complete list of trees, alignments and orthology predictions assigned to a given phylome. In this case only the best tree for each seed sequence is provided. The description gives a brief overview on the phylome and the date lets you know when the phylome was first build. Finally, the browse button will allow you to access the list of tree phylogenies.
The phylomeDB ID provides the internal phylomedb code of the seed sequence used to reconstruct a given tree. Left-clicking on it will lead you to the general sequence information page. Next to it you can find the links to the trees and alignments reconstructed for a given seed sequence in this phylome. The last column represents the additional information belonging to the seed sequence. This information is usually taken directly from the original proteome file.
As the list of phylomes grows, looking for a given phylome becomes more difficult. In the last version of phylomeDB we have created the collections, which join different phylomes that have a common theme, for easier access. Phylomes can be grouped because they belong to the same project (i.e. they were reconstructed for the quest for orthologs project Collection), they are reconstructed within the same species group (i.e. plants or fungi Collection) or they are reconstructed with the same species, just changing the species range included (i.e. Human Collection).
Left-clicking on the link of one of the collections will open a menu where a list of phylomes included in the collection can be found. In addition you can search specifically for proteins within a collection using the search space located on top of the phylome list. This search will limit the resulting trees to phylomes included in the collection. For a broader search the normal searchin tool should be used.
Data can be downloaded from phylomeDB for your use. There are several ways to do that depending on which information you wish to obtain:
- Tree page: if you only want information pertaining one particular protein you can obtain it from the individual phylomeDB tree page. The tabs called Download data.tar.gz, download OrthoXML or Image will all provide you with data.
- Phylome page: The "All phylomes" page will give a list of all publicly available phylomes. In addition it will provide links to download trees, alignments and orthology predictions for a given phylome.
- Downloads section: PhylomeDB has a ftp page that allow the user to donwload not only phylomes, but also code conversion files, the proteome fasta files that were used in the phylomes, and cross annotations to other databases, such as UniProt.