I have a lot of accession numbers that Im interested in. Is
there any easy way to retrieve them through Entrez, without having
to do individual searches for each one?
Yes, Batch Entrez allows you to do this. You can create a file containing
the list of accession numbers (or gi numbers), save it on your computer.
Click on the Batch Entrez link, which appears in the left-hand sidebar
of the Entrez screens. Enter the name of your file in the search
box, choose the Nucleotide or Protein database, and press Retrieve.
Then proceed as with any Entrez search to display and/or save the
How can I download the sequence immediately surrounding a particular
gene from the NCBI Human Genome Assembly?
Use the Human Genome Mapviewer. Search for the gene of interest using
its gene symbol and click on the link to the gene when the search
results are displayed. To retrieve a segment of sequence including
the gene, and both upstream and downstream regions, simply click on
the Download/View Sequence/Evidence link in the MapViewer.
To alter the segment downloaded, change the coordinates for the region
and press the Change Region button.
Can I use the e-PCR tool to design primers to amplify my gene of interest?
You wouldnt use e-PCR to design the primers per se, but you
can use it to see if the UniSTS database already contains a primer
pair that you could use to amplify your sequence.
The e-PCR service tool tests a DNA sequence for the presence of sequence
tagged sites by comparing the query sequence against the UniSTS database
of STS sequences and primer pairs. It looks for STSs in DNA sequences
by searching for subsequences that closely match the PCR primers in
UniSTS and have the correct order, orientation, and spacing that they
could plausibly prime the amplification of a PCR product of the correct
molecular weight. The output is a table of links to matching UniSTS
records, as well as the primer pairs and PCR conditions used to amplify
each STS identified.