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SV: Setting up a DNA sequencing facility

Dag Ahrén Dag.Ahren at mbioekol.lu.se
Thu Apr 13 04:54:28 EST 2000


<J.Theelen at antrg.azn.nl> skrev i
diskussionsgruppsmeddelandet:8cuv00$pi$1 at mercury.hgmp.mrc.ac.uk...
> Hi everyone,
>
> At the Universty Medical Centre Nijmegen, The Netherlands, we started a
few
> months ago with a central DNA sequencing facility. Therefore we have an
ABI
> 3700 sequencer and a MWG Biotech RoboAmp4200. Everything works just fine
and
> more and more departments of the university come to us with their samples.
>
> On this moment we use an Acces database where users can fill in the sample
data
>  before they bring them to us. Basecalling is performed by "sequencing
> analysis" and further data analysis (s.a. mutation detection) with
"sequence
> navigator".
>
> To improve these analysis steps we are planning to set up a server
(BioLIMS?)
> with the Staden software (and Phred to call the bases). The biggest issue
will
> be the automated but reliable detection of (heterozygous) point mutations
in
> big amounts of sample files (for the dept. of DNA-diagnostics). Is there
> anywhere somebody in Europe or US who has such a system working (i.e. in a
DNA
> diagnostic centre) ?
> -------------------------------------------------------------
>
> Joop P.G. Theelen
> University Medical Centre Nijmegen
> dpt. Human Genetics 417
> E-Mail j.theelen at antrg.azn.nl
>
>
> ---
>
Dear Joop,
in our group I am designing bioinformatics tools (focused on our EST
projects) for automatic handling of raw sequence data from ABI or MegaBace,
quality trimmed by Phred, translated to amino acid sequence for homology
searches against all publicly available databases and all results are
automatically put into a webbased relational database with hyperlinks to the
appropriate sequence hits. Your customers would only need to have a normal
web browser to get all information through inter- or intranet. It is easy to
add other software to the automated pipeline and there are a lot of useful
software availble to the scientific community. We are using Linux RedHat and
MySQL (relational database) on a normal PC which is the most cost effective
way to get fast and reliable biocomputing.

If you need some more details do not hesitate to email me.

Dag Ahrén
Microbial Ecology
Lund University
Sweden








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