Enhanced Entrez
Frequently Asked
Questions
Frequently Asked Questions
Is it possible to constrain a BLAST search to a particular taxonomic group, such as mammalia?
This is easily accomplished by using the organism filter box located in the middle of the Advanced BLAST page. Typing “mammalia” into this box will limit your BLAST search to the taxon Mammalia. To browse the NCBI taxonomic tree in order to determine which taxon to use, follow the link below the organism filter box entitled Explore the taxonomy database at NCBI.
RefSeq NM_xxxxxx and GenBank AFxxxxxx appear to be duplicates. Will one be removed?
No, both records will continue to be available. RefSeq and GenBank are separate databases, and both are included in the Entrez Nucleotides data set. RefSeq is a curated database in which each record encapsulates our current understanding of a gene, similar to a review article. In contrast, GenBank is an archival database where each record represents the work of a specific research group.
What is a taxonomy ID number (tax ID)?
The tax ID is a stable unique identifier for each taxon (for a species, a family, an order, or any other group in the taxonomy database). The tax ID apppears in the GenBank records as a “source” feature, e.g., /db_xref=“taxon: 9606” for Homo sapiens. Tax IDs can be used to retrieve sequences in Entrez with a syntax such as: txid9606[organism].
This will retrieve only Homo sapiens sequences. BLAST searches can also be limited to particular taxa by entering the tax ID into the organism filtering box.
How do I add a feature to my sequence submission using Sequin?
Once you have imported your sequence, use Sequin’s Annotate menu to see the list of standard features. Select the feature of interest from the submenus, for example, Coding Regions and Transcripts/CDS. This will invoke a feature-specific form that allows you to enter essential information about the feature and add it to your GenBank submission. To edit an existing feature, just double click on the feature. This will bring up a feature-specific form showing the current data, which can then be changed.
I have pasted a long sequence into ORF-Finder, but only want ORFs within a small block. Should I remove the surrounding sequence?
No, you can specify a nucleotide range using the “From” and “To” boxes below the query box. ORF-Finder will find ORFs only within the range specified.
