1. Browse. You can click the one of three pictrues to browse by classifications or species of animals & fungi or plants in the middle of the "browse" webpage. Then a clear page is showed with a detailed treeview and a big and clear picture of phylogenetic tree. Please click the names on the left treeview or small logos on the right picture to browse each family or species.

2. Search. You can input one or multiple keywords (separated by space character) to search the UUCD 1.0. The search fields including UUCD ID, UniProt ID, Ensembl ID, Protein Name, Protein Alias, Gene Name, Gene Alias, and Modfication.

EXAMPLE: Please click on the "Example" button to search "TRCP" in Gene Name field. By clicking on the "Search" button, the related UUCD proteins will be shown.

3. Advance Options. Three advance options are provided, including advance search, BLAST search, and HMM search.

(1) Advance search. You can input up to three terms to search the more specifical information. The query fields can be empty if less terms are needed. The three terms could be connected by the following operators:

exclude: If selected, the term following this operator must be not contained in the specified field(s)
and: the term following this operator has to be included in the specified field(s)
or: either the preceding or the following term to this operator should occur in the specified field(s)

EXAMPLE: You can click on the "Example" button to load an instance, which could search a E3 ligase in Homo sapiens. The H. sapiens FBW1A (UUC-HoS-00457) will be shown by clicking on the "Submit" button.

(2) BLAST search. You can input a sequence to find the specific protein and/or related homologues by sequence alignment. This search-option will help you to find the queried protein accurately and fast. Only one protein sequence in FASTA format is allowed per time. The E-value threshold could be user-defined, while the species information could be specified. The default parameters of E-value and species are 0.01 and H. Sapiens, respectively.

EXAMPLE: You can click on the "Example" button to load the protein sequence of human F-box/WD repeat-containing protein 1A. By clicking on the "Submit" button, you can find the related homologues in H. Sapiens.

(3) HMM search. You can find the specific domain or motif of a protein sequence by HMM algorithm. This search-option will help you to find the detailed positions of the queried domains accurately. Only one protein sequence in FASTA format is allowed per time. the E-value threshold is internally defined. There are not a same E-value threshold for all domain-based HMM profiles. Every E-value threshold is corresponding to a particullar domain model. For instance, the E-value threshold of Cullin domain is 1e-5, and the E-value threshold of HECT domain is 1e-11.

EXAMPLE: You can click on the "Example" button to load the protein sequence of human U-box domain-containing protein 5. By clicking on the "Submit" button, you can find the related domain information in HMM search result.

If any question, please contact the four major authors: Tianshun Gao, Zexian Liu, Dr. Jian Ren and Dr. Yu Xue for details.