Searching DIP

• Node Search
  Node search allows one to find DIP entries using cross-references to other databases or by searching protein annotation local to the DIP database.

  Node ID search can identify a DIP node through a reference to a specific entry in a number of databases including SwissProt, PIR, NCBI and cross-references therein. It is also possible to specify a particular DIP node (please, use DIP:310N format) or GI code (use gi:71632 format).

  Note, that, as DIP nodes are cross-referenced to SwissProt and thus to a number of well-known domain (eg ProDom, Pfam) and motif (eg Prosite, Prints) databases, it is possible to search the database for all the entries that contain a specific domain or motif. Please, specify an appropriate identifier from one of those databases to retrieve a list of matching entries.

  Local Annotation search can identify a DIP node or a list of nodes based on a match to an annotation local to DIP. It is possible either to specify desired values of selected fields within the database (eg Protein Name, Species, etc) or to search all the fields within the database at once for the occurence of a term specified in Any Field. The fields marked with ! accept complex, logical expressions that follow the syntax below:

  Operator	Operation	Example (Name/Description field)
  		Query	Result
  OR	logical OR	actin OR myosin	All the actins and myosins within DIP. Note, that exact match to each keyword is required. Therefore, 'actin' but NOT 'actin-capping' proteins will be found.
  AND	logical AND	receptor AND interferon gamma	All interferon gamma receptors. Note, that exact match to entire 'interferon gamma' term (including single space) is required.
  NOT	logical NOT	receptor AND interferon AND NOT gamma	All the receptors for interferons other than gamma.
  '(' & ')' (brackets)	operator precedence	receptor AND (interferon OR growth factor)	All the interferon and growth factor receptors.
  %	wild-card character	(A) actin% (B) %actin% (C) %actin	All the entries matching 'actin' (A,B,C) but also 'actin-capping' (A,B), 'actin-related' (A,B), 'prolactin' (B,C), etc. When % is not given at either end of a keyword it is expected to be preceded/succeded by a space.

• BLAST Search
  
  BLAST search looks for proteins with sequences related to the query sequence. All the proteins with p-values better than 10^-5 are reported.

• Text Search (deprecated)
  Text search allows one to specify a string in order to find all DIP entries (nodes or edges) with description that matches the text entered in the appropriate fields of the search form.

  NOTE: Use Text Search at your own risk!!! At the moment, this option can generate extremely slow searches. It will be gradually replaced with faster alternatives.

The output of each search provides a list of the proteins found. Links to detailed information about each protein and to the interactions it participates are also provided as well as links to the corresponding SwissProt, PIR and NCBI entries.