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In dbPAF 1.0 database, we tried to make it more powerful and convenient to be used. The dbPAF 1.0 provide the search option and advanced options.

1. Search.You can input one or multiple keywords (separated by space character) to search the dbPAF database. The search fields including dbPAF ID, UniProt Accession, Protein Name, Protein Alias, Gene Name, Gene Alias, Species, and Function.

Example: Please click on the "Example" button to search "P53_HUMAN" in UniProt Accession field. By clicking on the "Submit" button, the related proteins will be shown.

2. Browse. You can browse the dbPAF 1.0 database by species.

Browse by species: You can select one of these seven species listed below to browse all known proteins with p-sites of corresponding species.

3. Advanced Options. Three advanced options are provided, including advanced search, batch search, BLAST search.

(1) Advanced search allows you to input up two or three terms to find the information more specifically. The querying 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 Phosphoprotein p53 in Homo sapiens. The human Phosphoprotein p53 will be shown by clicking on the "Submit" button.

(2) Batch search could be used to find a number of proteins such as a protein list. You can input keyword list, for example, a list of UniProt IDs to search the database. The list should be inputed as one keyword one line.

Example: You can click on the "Example" button to load three proteins UniProt accessions including P04637,YI066 and F8WH10. By clicking on the "Submit" button, you can find "Cellular tumor antigen p53", "Putative uncharacterized membrane protein YIL066W-A" and "Vascular endothelial growth factor A".

(3) BLAST search could be used to find the specific protein and/or related homologues by sequence alignment. This search-option will help you to find the querying protein accurately and fast. Only one protein sequence in FASTA format is allowed per time. The E-value threshold could be user-defined. The default parameters of E-value is 0.01.

Example: You can click on the "Example" button to load the protein sequence of Homo sapiens Phosphoprotein p53. By clicking on the "Submit" button, you can find the related homologues.