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Transitioning from LocusLink to Entrez Gene

Cancer Chromosomes: a New Entrez Database

HomoloGene: An Entrez Database with a New Look

BLAST Link (BLink) to Protein Alignments and Structures

Debut of the HCT Database and Anthropology/Allele Frequencies in dbMHC

350kb Sequence Length Limit Removed by Sequence Database Collaboration

New Eukaryotic Genomes at NCBI

Environmental Samples Make Big Splash

HIV Protein-Interaction Database

e-PCR and Reverse e-PCR: Greater Sensitivity, More Options

New Organisms in UniGene

RefSeq Accession Numbers Get Longer as Rat Gets Last 6-digit Accession

Slots available for FieldGuidePlus Training Course Onsite at NCBI

RefSeq Release 6 on FTP Site

Exponential Growth of GenBank Continues with Release 142

Entrez Tools is a 'Hot Spot'

BLAST Lab: Using BLASTClust

New Microbial Genomes in GenBank

Entrez Quiz

Masthead





e–PCR and Reverse e–PCR: Greater Sensitivity, More Options

Electronic PCR (e-PCR) is used to identify sequence landmarks called Sequence Tagged Sites (STSs) within a nucleotide sequence. Electronic-PCR works by looking for matches to STS primer pairs with the orientation and spacing required to produce an amplicon of the expected size.

Two types of e-PCR can now be performed from the e-PCR home page: the original, Forward e-PCR, and a new application, Reverse e-PCR. Forward e-PCR is used to determine if a user-supplied nucleotide sequence contains any known STS. Queries are made against the markers in NCBIs UniSTS database, a public collection of PCR primer pairs used in mapping and other types of genome analysis for a wide range of organisms. UniSTS contains over 270,000 markers and includes data from the STS division of GenBank, The Radiation Hybrid Database, The Genome Database, Mouse Genome Informatics, the Rat Genome Database, Zebrafish Information Network and PubMed Central. If an STS is found using the online version of Forward e-PCR, the chromosomal location and a link to UniSTS are provided. Mapped markers can be displayed from UniSTS reports using the MapViewer and viewed in the context of the other available genomic data.

To improve the sensitivity of a Forward e-PCR search, there is now an option to search using discontiguous, or imperfect, matches between the query sequence and the STSs in UniSTS. To increase the probability of finding STSs that may have been missed with the contiguous word option, the size of the segment to be matched, called the word size, number of allowable mismatches, and number of permissible gaps can be adjusted. The size of the STS can also be adjusted in order to allow for deviations which may arise from the amplification of a region in the genome that shows length polymorphism.

Reverse e-PCR can be used to estimate the genomic binding site, amplicon size and specificity for user-supplied primer pairs. The Reverse e-PCR query page can accept up to 20 primer pairs or STS identifiers as input for searches against organism-specific databases. Primer pairs or STS identifiers can be searched against the genomic and transcript databases of Anopheles gambiae, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Homo sapiens, Mus musculus and Rattus norvegicus.

Interested in seeing how the forward and reverse e-PCR tools work? Try your hand at some of the e-PCR examples that are provided on the two search pages found at:


For those who need to perform large batches of searches or who need to search a custom database, a standalone version of e-PCR has been developed for the Windows, Linux and Unix operating systems. These binaries, along with the source code for compiling e-PCR on other operating systems, are available via FTP at:


—SD

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NCBI News | Fall/Winter 2002 NCBI News: Spring 2003