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
FASTA - definition line and sequence character format
Graphics - diagram of annotation in graphical sequence viewer
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.