Conducting a search in the NCBI Database from CLC Genomics Workbench corresponds to conducting search for structures on the NCBI's Entrez website. When conducting the search from CLC Genomics Workbench, the results are available and ready to work with straight away.
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.
You can append a wildcard character by clicking the checkbox at the bottom. This means that you only have to enter the first part of the search text, e.g. searching for "prot" will find both "protein" and "protease".
The following parameters can be added to the search:
- All fields. Text, searches in all parameters in the NCBI structure database at the same time.
- Organism. Text.
- Author. Text.
- PdbAcc. The accession number of the structure in the PDB database.
The search parameters are the most recently used. The All fields allows searches in all parameters in the database at the same time.
All fields also provide an opportunity to restrict a search to parameters which are not listed in the dialog. E.g. writing 'gene[Feature key] AND mouse' in All fields generates hits in the GenBank database which contains one or more genes and where 'mouse' appears somewhere in GenBank file. NB: the 'Feature Key' option is only available in GenBank when searching for nucleotide structures. For more information about how to use this syntax, see http://www.ncbi.nlm.nih.gov/entrez/query/static/help/Summary_Matrices.html#Search_Fields_and_Qualifiers
When you are satisfied with the parameters you have entered click Start search.
Note! 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.