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The Nucleotide, Genome Survey Sequence (GSS), and Expressed Sequence Tag (EST) database all contain nucleic acid sequences. The data in GSS and EST are from two large bulk sequence divisions of GenBank. GSS and EST data are typically uncharacterized, short genomic (GSS) or cDNA (EST) sequences.
Searching any of the three databases will provide links to results in the other. Unless you know that you are trying to find a specific set of EST or GSS sequences, searching the Nucleotide database with general text queries will produce the most relevant results. You can always follow links to results in EST and GSS from the Nucleotide database results.
How do I use a simple query, such as a word or a phrase?
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To search data in the nucleotide or protein databases enter a general text query to the search field, select the database and click on the Search button. You can use a protein name, gene name, or gene symbol directly. Searching with a submitter or author name in the following format will produce the best results.
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Smith JR (last name followed by initials, no punctuation)
Database identifiers such as accession numbers or gi numbers will directly retrieve the full sequence record.
CAA79696
NP_778203
263191547
BC043443
NM_002020To find a match to an exact phrase, enclose it in quotation marks.
"contactin associated protein"
"duchenne muscular dystrophy"How can I make my search more specific with Boolean operators (AND, OR, NOT)?
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Use the boolean operator AND to find records that contain every one of your search terms, the intersection of search results.
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Use the
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boolean operator OR to find records that include one of several search terms, the union of search results.
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contactin OR neurofascin Protein Nucleotide
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Use the boolean operator NOT to exclude records matching a search term
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contactin NOT neurofascin Protein Nucleotide
How do I restrict my search to specific subsets of records such as those from a specific organism, molecule type, source database, genomic or cDNA library name or properties?
You can use the Limits page to limit your search to only certain kinds of records. You can also use the Filter your results to select categories of records after a search. Follow these links to jump to the limit of interest: organism, molecule type, source database, library name or properties.
Limits
Use the Limits page linked to top of any of the Protein, Nucleotide, GSS, or EST webpages to select the appropriate limit from the various pull-down lists.
To fetch data select the File ‣ Access remote database... item in the main menu.
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To limit results use the Result limit field.
After you click the Search button, UGENE searches the biological objects and shows it in the Results field. You can download the object(s). Select one or several objects (for selecting several objects use the Ctrl button) and click the Download button. The dialog will appear:
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Here you need to enter unique id of the biological object and choose a database. Unique identifiers are different for various databases. For example, for NCBI GenBank such unique id could be Accession Number or NCBI GI number.
Optionally, you can browse for a directory to save the fetched file to.
After you click the OK button, UGENE downloads the biological object (DNA sequence, protein sequence, 3d model, etc.) objects and adds it to the current project.If something goes
wrong check the Log View, it will help you to diagnose the problem.