NCBI search options
Conducting a search in the NCBI Database from CLC Sequence Viewer corresponds to conducting the search on NCBI's website. When conducting the search from CLC Sequence Viewer, the results are 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 Sequence Viewer 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 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). - Organism
- Definition/Title
- 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
- Accession
Note! 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
http://www.ncbi.nlm.nih.gov/books/NBK3837/
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.