GenBank search options
Conducting a search in the NCBI Database from CLC Genomics Workbench corresponds to conducting the search on NCBI's website. When conducting the search from CLC Genomics Workbench, the results are available and ready to work with straight away.
You can choose whether you want to search for nucleotide sequences or protein sequences.
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.
Note! 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.
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".
The following parameters can be added to the search:
- All fields. Text, searches in all parameters in the NCBI database at the same time.
- Organism. Text.
- Description. Text.
- Modified Since. Between 30 days and 10 years.
- Gene Location. Genomic DNA/RNA, Mitochondrion, or Chloroplast.
- Molecule. Genomic DNA/RNA, mRNA or rRNA.
- Sequence Length. Number for maximum or minimum length of the sequence.
- Gene Name. Text.
gene[Feature key] AND mousein All fields generates hits in the GenBank database which contains one or more genes and where 'mouse' appears somewhere in GenBank file. You can also write e.g.
CD9 NOT homo sapiensin All fields.
Note! The 'Feature Key' option is only available in GenBank when searching for nucleotide sequences. For more information about how to use this syntax, see http://www.ncbi.nlm.nih.gov/books/NBK3837/
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.