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  In silico experiments with bacteria: PCR, AFLP-PCR and PFGE

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Author Topic:   In silico experiments with bacteria: PCR, AFLP-PCR and PFGE
Joseba Bikandi
posted 06-20-2003 10:34 AM     Click Here to See the Profile for Joseba Bikandi   Click Here to Email Joseba Bikandi     Edit/Delete Message Reply w/Quote
Dear Colleagues,

We have developed a WWW server (www.in-silico.com) which performs three
interesting tasks for molecular epidemiology typing by using up-to-date
completely sequenced bacterial genomes (119 genomes at this moment):

1) in silico PCR amplification,

2) in silico AFLP-PCR, and

3) restriction digest of complete genomes and PFGE.

In theoretical PCR, after selection of genome and introduction of primers, the
resulting PCR amplification is shown as an image, and fragments size,
DNA sequence and corresponding ORF identity of each amplicon is easily
available. Plasmids of sequenced species may be included in the

Theoretical AFLP-PCR will also provide identical information
as PCR amplification, and amplification with selected restriction
enzymes is also shown as an image. Additionally, an AFLP-PCR suggestion tool
provides a list of commercial restriction enzyme pairs, which may be
used to yield up to 50 amplicons in the selected genome without needing
to perform a selective amplification.

Restriction digest of complete genomes and plasmids provides the number
of cutting sites for restriction enzymes, and when the number of fragments
generated is 50 or fewer, PFGE image and restriction maps are provided.

Additional general tools has been also included in this site:

a) ORF search by name within a specific genome,

b) DNA to protein translation script which allows translation by using
13 different genetic codes or a user defined genetic code, and

c) restriction digest of DNA with all commercially available restriction enzymes.

All this tools are of great interest for researches willing to probe out
of the bench these techniques, and they are freely available online at www.in-silico.com.

Dr. Joseba Bikandi
Department of Immunology, Microbiology and Parasitology
Faculty of Pharmacy
University of the Basque Country


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