Conducting a search using Search for Sequences at NCBI corresponds to using the same query terms on the NCBI website. For example, searching the nucleotide database corresponds to a search at https://www.ncbi.nlm.nih.gov/nucleotide/. A list of the entries matching the search terms is returned. Those of interest can then be selected and then downloaded, ready for downstream use in the Workbench.
Click on Add search parameters to add parameters to your search. The following are available:
- All Fields Searches for the terms provided in all fields of the NCBI database.
- Modified Search for entries modified within the period specified from a drop-down list.
- Gene Location Choose from Genomic DNA/RNA, Mitochondrion, or Chloroplast.
- Molecule Choose from Genomic DNA/RNA, mRNA or rRNA.
- Sequence Length Enter a number for a maximum or minimum length of the sequence.
- Gene Name
Check the "Append wildcard (*) to search words" checkbox to indicate that the term entered should be interpreted as the first part of the term only. E.g. searching for "genom" with that box checked would find entries starting with that term, such as "genomic" and "genome".
When you are satisfied with the parameters you have entered, click on the Start search button.
Feature keys can be added when searching for nucleotide sequences. Writing
gene[Feature key] AND mouse
searches for one or more genes and where 'mouse' appears somewhere in the entry. For more information about how to use this syntax, see http://www.ncbi.nlm.nih.gov/books/NBK3837/
Where multiple terms are entered into a single field, the terms are usually treated as if they have an AND between them, which means that entries returned must contain all the specified terms. A notable exception is if multiple accessions are listed in an "All Fields" search field, in which case a results for each valid accession listed is returned.
You can add the words "AND", "OR" or "NOT" to the terms in a given field to further customize your search. Further details about searching Entrez sequence databases can be found at https://www.ncbi.nlm.nih.gov/books/NBK44864/.