Searching the Entrez database

The MacVector interface searches the database in discrete sections, allowing you to search the full range of information available.

1. Choose Database | Online Keyword Search for Sequences (Entrez).

The Internet Entrez Browser window is displayed.

When run for the first time in a session MacVector will contact the NCBI for an updated list of available databases. Once this has been received choose the appropriate database that you wish to search.

The drop-down menus enables you to define a single or combined (Boolean) annotation search of the database. Two of the drop down menus contain a list of all possible search categories for the portion of the database you are searching. The central drop-down menu contains logical operators that enable you to perform more complicated searches using two criteria. For example, you could extract all ribosomal protein sequences from the organism "Canis" by searching for "canis*" in the organism field, the AND operator and "ribosomal" in the indexed words field.

To search in a single category

Select a search category in the first drop-down menu.
In the adjoining text box, type the required search text. You can use the ? wildcard character to substitute for single characters and * to substitute for any number of characters. Only one string is allowed as a search query for each field, except for the entry definition field, when separate search strings can be separated by a single space.
Then select Search to perform the search.

During the search, the Search button label changes to Stop, allowing you to stop a search. If MacVector finds any matches to your query string,it will list the matches in the middle section

TIP: You can view a detailed report on a single hit by selecting it and choosing the Details button.

To search with multiple categories

Enter the first search term as above.
Click the "+" button at the end to add an additional search term line.
Choose the logic for the additional term from AND OR or NOT.
Enter the rest of the search term.
Repeat steps 2 to 4 for additional search terms.
Select Search to perform the search.

During the search, the Search button label changes to Stop.

Note: that if you want to use the Sequence Length query line you must use range of lengths separated by a colon. e.g. 1000000:2000000 for sequences between 1Mb and 2Mb. Also note that only simple boolean expressions are supported. Nesting is not supported and expressions are evaluated left to right. For example the following line

Saccharomyces cerevisiae[Organism] OR Schizosaccharomyces pombe[Organism] AND adh1will find "ADH1" in either of the two yeasts.

If MacVector finds any matches to your query string, it will list the hits or matches in the middle section.

Searching the Entrez database

To search in a single category

To search with multiple categories

Related Topics.