Conducting a search in the NCBI Database from CLC Genomics Workbench corresponds to conducting the search on NCBI's website, while having the results available and ready to work with straight away.
You can choose whether you want to search for nucleotide sequences, protein sequences or EST databases.
As default, CLC Genomics Workbench offers one text field where the search parameters can be entered. Click Add search parameters to add more parameters to your search. The search is a "and" search, meaning that when adding search parameters to your search, you search for both (or all) text strings rather than "any" of the text strings.
The following parameters can be added to the search:
- All fields Searches in all parameters in the
NCBI database at the same time. It also provide an opportunity to search to parameters which are not listed in the dialog (e.g.,
CD9 NOT homo sapiens).
- Modified Since Choose one option from the drop-down menu, between 30 days and 10 years.
- 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
You can append a wildcard character by checking the checkbox at the bottom. This means that you only have to enter the first part of the search text, e.g., searching for "genom" will find both "genomic" and "genome".
A "Feature Key" option is available in GenBank when searching for
nucleotide sequences: writing
gene[Feature key] AND mouse will generate
hits for one or more genes and where 'mouse' appears somewhere in GenBank file.
For more information about how to use this syntax, see
When you are satisfied with the parameters you have entered, click Start search. When conducting a search, no files are downloaded. Instead, the program produces a list of links to the files in the NCBI database. This ensures a much faster search.