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NCBI Resources

Information about determining the best databases to use to answer questions and reviews of commonly used databases.

Where to look for answers outside of Protein

Q: What are the important functional components of my protein, and where are they located?

A: Use CD-Search and Conserved Domain Database.

Q: Is there a structure for my protein?

A: Use CD Search or BLASTp.

Q: Where does a given variation (SNP) occur in the structure?  Can you tell me what it does?

A: Determine the location of variant within the structure in SNP --> Follow links to Conserved Domains to load alignments --> Evaluate SNP position relative to functional elements.

Protein Views

GenPept - NCBI file format

Cytochrome B protein in GenPept NCBI File format

 

FASTA - definition line and sequence character format

Cytochrome B FASTA View

Graphics - diagram of annotation in graphical sequence viewer

Cytochrome B Graphics View

Filters after search

  • Species
  • Source databases
  • Genetic compartments
  • Enzyme types
  • Sequence length
  • Molecular weight
  • Release data
  • Revision date
  • Search fields

Fields

All sequence databases have the following advanced fields:

  • Organism [ORGN] scientific and common names for the complete taxonomy of organisms that are the source of the sequence records. 
    • Example: cellular organisms [ORGN]
  • Gene Name [GENE] Gene names are annotated on database records. 
    • Example: BRCA1[GENE]
  • Modification Date[MDAT] the date of the most recent modification of a sequence record.  Date format is YYYY/MM/DD.  Only year is required.  Modification date is often used as a range of dates, the colon ( : ) separates the beginning and end of a date range.
    • Example: 2010/01:2010/12/31[MDAT]
  • Filter[FILT] filtered subsets of the database.  Important kind of filter is based on the presence of links to other records.
    • Example: protein_structure[FILT]

You can see a complete list of fields and examples of their use in a search by going to the "Search Field Descriptions" pamphlet in NCBI Bookshelf.