PhylomeDB: Difference between revisions
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* '''Orthology prediction''': Orthology predictions are provided for all the phylomes in which the query protein appears. The results are formated into a table. The first table accounts for all the orthology predictions in all phylomes while the remaining tables separate those predictions by phylome. | * '''Orthology prediction''': Orthology predictions are provided for all the phylomes in which the query protein appears. The results are formated into a table. The first table accounts for all the orthology predictions in all phylomes while the remaining tables separate those predictions by phylome. | ||
[[File:PhylomeDB.0018.png|400px|center]] | |||
[[File:PhylomeDB. | PhylomeDB also allows for searches using the Blast Search! option. Clicking on the Blast search button will open a box in which a protein sequence can be introduced and a standard Blast search will be executed. | ||
The image below shows the use of Blast to query PhylomeDB. The blast search only returns proteins that have been used as seed protein in one of the phylomes and that are homologous to the query protein. The results are formatted into a table where the different entries show the name of the seed proteins, the phylomes in which it appears and the different statistics that results from the blast search. Selecting any of the resulting entries will provide a page like the one described above. | |||
[[File:PhylomeDB.0019.png|400px|center]] | |||
===Usage examples=== | ===Usage examples=== | ||
Revision as of 13:06, 7 July 2009
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| Link/URL: | |
|---|---|
| What: |
A database for genome-wide collections of gene phylogenies. |
| Who: |
Comparative Genomics Group at CRG (Barcelona, Spain). |
| Updates: | |
| Upcoming events: | |
| Web Services: |
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| edit table |
About PhylomeDB
Add general information here [link PhylomeDB] is...[1]
Content
Using PhylomeDB
Browsing
Searching
You can search for a protein using the phylomeDB's quick search box. Proteins codes that work in PhylomeDB include the internal Phylome ID, Ensembl, SwissProt, SwissProt TrEMBL or NCBI NonRedudant IDs. Once the user performs a search and retrieves the entry/entries that match the query, the web user gets a entry which has the following parts (see image below):
- Basic protein information: Information about the query protein that includes the protein sequence and any comments retrieved from the original proteome database. There may be more than one entry for a given protein ID if two or more proteomes of the same species have been used in PhylomeDB.
- Seed trees: All trees in which the query protein has been used as seed protein to generate the trees.
- Collateral trees: All trees where the query protein appears but was not used as seed.
- Orthology prediction: Orthology predictions are provided for all the phylomes in which the query protein appears. The results are formated into a table. The first table accounts for all the orthology predictions in all phylomes while the remaining tables separate those predictions by phylome.
PhylomeDB also allows for searches using the Blast Search! option. Clicking on the Blast search button will open a box in which a protein sequence can be introduced and a standard Blast search will be executed.
The image below shows the use of Blast to query PhylomeDB. The blast search only returns proteins that have been used as seed protein in one of the phylomes and that are homologous to the query protein. The results are formatted into a table where the different entries show the name of the seed proteins, the phylomes in which it appears and the different statistics that results from the blast search. Selecting any of the resulting entries will provide a page like the one described above.
Usage examples
Add links to additional pages describing success stories here.
Technology
Web Services/API
Discussion
References
See Help:References for how to manage references in EcoliWiki.
External Links
[link PhylomeDB] URL:link