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In this issue

Using TaxPlot to
Compare Genomes

New RefSeq Accession
Numbers for Curated
Genomic Regions

GenBank News

Recent Publications

DART Targets
Protein Domains

Evidence Viewer
Facilitates Analysis
of NCBI Human
Gene Models

Frequently Asked



Frequently Asked Questions Banner



I have a lot of accession numbers that I’m 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 results.

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 wouldn’t 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.

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NCBI News | Fall 2001 NCBI News