ProtozoaDB 2.0 beta (2013)

The ProtozoaDB database can be searched using (i) protein name [By name], (ii) identifier [genbank accesion number or genbank ID], (iii) similarity [By Blast] and (iv) EST keyword [By EST]

ProtozoaDb Home

ProtozoaDB is fully based on web 2.0 technologies, then you can find a Tag Cloud at the right side of the website. Everytime users search the database "By Name" the Tag Cloud list is updated, the bigger the font of the protein name in the Tag Cloud, the more "searched" it has been.

If you click in the "fibrillarin" Tag you get a list of Protozoan proteins with the word "fibrillarin" in the definition


Fibrillarin tag cloud


From the fibrillarin results list, you can choose the AAB86601.1 cyclophilin from Entamoeba by clicking in the "details" hyperlink, then a number of webservices are triggered to get information from ProtozoaDB, PDB, KEGG and PubMed (represented by horizontal tabs)

Cyclophilin tag cloud results


In the ProtozoaDB horizontal tab, you will find results stored locally in the ProtozoaDB database, for example orthologs proteins identified by OrthoSearch. Those identified orthologs have a link to their correspondent HMMER profile (built by us). You can dowload those HMMER profiles to be used in further searches and your own data.

Cyclophilin orthologs


Conserved Domain best his are also listed (Top 10 rpsBlast searches)

Cyclophilin Conserved Domains


You will know if you protein of interest has similarity with the human proteome as the Top Ten BlastP hits are also listed

Cyclophilin hits with human proteome



A list of orthologous cyclophilin proteins in Protozoan genomes is displayed, then you can view the orthologs member by clicking in "Group". Finally, a list of Top 10 BlastX hits of cyclophilin with Protozoan EST is also displayed.


Cyclophilin orthologs by OrthoMCL


In the PDB horizontal tab, you will find webservices results from 2 similarity algorithms available at PDB: (i) BLAST against PDB and (ii) FASTA against PDB. Pass the mouse over the BLAST PDB hit description to see details as the organism name of the hit

DNA Polymerase Blast Hits with PDB



The PDB-FASTA webservice shows the best FASTA hits with protein structures

DNA Polymerase FASTA Hits with PDB


The KEGG webservice will show all KEGG pathways where cyclophillin is found


DNA Polymerase KEGG Pathways


The NCBI horizontal tab shows webservices results of the published paper that originated the protein being analyzed (in this example DNA polymerase). An additional search is performed at PubMed using the protein name and organisn name, so even there is no publication directly assoctiated with the protein, users will still get related publications.


DNA Polymarase Literature


ProtozoaDB allows users to query the database using BlastP, just paste your protein in fasta format, then click "Go", and a list of similar proteins will be displayed.

DNA Polymerase BlastP results

If you click on "Blast Result"a full BlastP hits list will be displayed in a new window


DNA Polymerase Full BlastP Results

Once you query ProtozoaDB by BlastP, you can choose one protein from the list and ask for "details"then you will trigger again all the webservices and obtain detailed information from that protein.

Selecting a protein from Full BlastP Results

The current version of ProtozoaDB allow users to query Protozoan EST hits against Uniref-90. In our database only T. rangeli EST has CDS avaliable, then only T. rangeli EST are displayed in the results. We are improving this search then all Protozoan EST (not only T. rangeli) will be displayed in the near future

Oxiredutase EST search
RESTful webservices

ProtozoaDB can be query by a number of REST-based webservices (eg: byBlast, byCdd, byEst, byGI, byId, byOrthoMCL, byProduct, cdd, details, estSimilarity, estUniref90, getGenbankGI, homoSapiens, orthoMCL, orthoSearch, orthoSearchVerify, orthoSearchVerifyByNCBITaxonId). The details on how to use these webservices will be posted here soon.

Reference

If you use ProtozoaDB please kindly cite it properly:

Dávila AM, Mendes PN, Wagner G, Tschoeke DA, Cuadrat RR, Liberman F, Matos L, Satake T, Ocaña KA, Triana O, Cruz SM, Jucá HC, Cury JC, Silva FN, Geronimo GA, Ruiz M, Ruback E, Silva FP Jr, Probst CM, Grisard EC, Krieger MA, Goldenberg S, Cavalcanti MC, Moraes MO, Campos ML, Mattoso M.
ProtozoaDB: dynamic visualization and exploration of protozoan genomes.
Nucleic Acids Res. 2008 Jan;36(Database issue):D547-52. Epub 2007 Nov 2.


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