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   Electronic PCR

PCR-based sequence tagged sites (STSs) have been used as landmarks for construction of various types of genomic maps. Using "electronic PCR", these sites can be detected in DNA sequences, potentially allowing their map locations to be determined. Because informative microsatellites can be found in every kb or so of DNA sequence, it should be possible to use the map and progeny to position contigs that are not recognized by electronic PCR with listed primers.

References

  • Schuler G.D. Sequence mapping by Electronic PCR. Genome Res 1997; 7:541-550. PubMed
  • Schuler, GD. Electronic PCR: bridging the gap between genome mapping and genome sequencing. Trends Biotechnol 1998; 16(11):456-9. PubMed

The Electronic PCR web version is available at: http://www.ncbi.nlm.nih.gov/genome/sts/epcr.cgi and takes Accession/GI or FASTA sequences (use the copy/paste method or take an input file from your computer). The Electronic PCR web version currently does not allow changes to the default option values.

Note: June 13, 2003: e-PCR version 1.2.0 is released rewritten in C++.. ftp://ftp.ncbi.nih.gov/pub/schuler/e-PCR/

The older e-PCR program June 17, 1998 is still available:
ftp://ftp.ncbi.nih.gov/pub/Malaria/e-PCR/ and uses specific Malaria samples. Only the local stand-alone "e-PCR" version allows for mismatch. Keep in mind that exact matches to both forward and reverse primers give a robust criterion, whereas mismatches give a great potential for false positives. Therefore, users of the local e-pcr program need to evaluate the output critically.

Frequently Asked Questions (FAQ)

Revised: June 16, 2003

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