April 7, 1999
Dear Dr. Bernd Weisshaar,
I read your posting to the ABRF list server and
am very familiar with your software requirements.
I have developed custom Web based bioinformatics solutions
for DNA, EST, and Protein research for the last three years.
Highlights of my dnaLIMS system includes functionality to:
Runs on Sun UNIX computers with Apache Web server,
Track physical samples,
Organize and manage sample requests,
Create sample sheets,
Post process ABI Run Folder files,
Store and manage access to sequence files,
Store and manage access to electropherograms,
Create local sequence libraries (Genbank and GCG format),
Provide Blast capability against Genbank or Local Libraries
(As the Gel is processed into LIMS, and on-demand in real time).
Easily interfaces to upstream sequence analysis tools. i.e., GCG.
I developed an EST LIMS system similar to dnaLIMS that has a custom
sequencing request form that automatically:
Creates a sample sheet for a 96 lane Gel,
Has intellegence built into the sample names,
Supports positioning a Control Sample in any/multiple lanes,
Of your requirements:
1. Those features that are currently supported include:
- runs on UNIX
- performes BLAST against local data bases
- displays the results via a WWW interface
- selects significant hits (cut-off by user-defined criteria)
- re-runs the BLAST in a time-dependent way
2. Those features that are in the current development cycle:
- does vector trimming in a project-specific way
- allows text-based searches of the annotation data of hits
3. Those features that require development scheduling:
- combines data from both ends of the cDNA (5-prime and 3-prime
sequences)
More information is available on my web site:
http://www.dnatools.com
I am attending a conference in England and will return April 16, 1999.
I can provide more system information and would be happy to discuss
your needs and my software solution when I return.
Thank you,
Jerry Tuneberg
970-689-9268 p
970-226-8723 f
jerryt@dnatools.com
Bernd Weisshaar wrote:
> Dear Sequers & BLASTers,
>
> we have recently faced the problem that more and more of our our custom=
es
> want to do small EST projects of a few hundert to up to 10000 ESTs. The
> generation of the primary data works nice, but the data analysis side o=
f
> things is a problem.
>
> I am looking for software which does the following (hints on partial
> solutions also wellcome!):
>
> - runs on UNIX
> - does vector trimming in a project-specific way
> - combines data from both ends of the cDNA (5-prime and 3-prime sequenc=
es)
> - performes BLAST against local data bases
> - displays the results via a WWW interface
> - selects significant hits (cut-off by user-defined criteria)
> - allows text-based searches of the annotation data of hits
> - re-runs the BLAST in a time-dependent way
>
> Obviously, the task list can be made longer, but ....
>
> Thanks and best regards, Bernd
> _____________________________________________________________________
>
> PD Dr. Bernd Weisshaar
> MPI fuer Zuechtungsforschung
> Carl-von-Linn=E9-Weg 10
> 50829 Koeln
> Germany
>
> Tel. office: +49-221-5062 590 Tel. lab: +49-221-5062 311
> Fax: +49-221-5062 313
> e-mail: weisshaa@mpiz-koeln.mpg.de
> WWW-URL: http://www.mpiz-koeln.mpg.de/~weisshaa/BW-info.htm
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April 7, 1999
Dear Dr. Bernd Weisshaar,
I read your posting to the ABRF list server and
am very familiar with your software requirements.
I have developed custom Web based bioinformatics solutions
for DNA, EST, and Protein research for the last three years.
Highlights of my dnaLIMS system includes functionality to:
Runs on Sun UNIX computers with Apache Web server,
Track physical samples,
Organize and manage sample requests,
Create sample sheets,
Post process ABI Run Folder files,
Store and manage access to sequence files,
Store and manage access to electropherograms,
Create local sequence libraries (Genbank and GCG format),
Provide Blast capability against Genbank or Local Libraries
(As the Gel is processed into LIMS, and on-demand in real time).
Easily interfaces to upstream sequence analysis tools. i.e.,
GCG.
I developed an EST LIMS system similar to dnaLIMS that has a custom
sequencing request form that automatically:
Creates a sample sheet for a 96 lane Gel,
Has intellegence built into the sample names,
Supports positioning a Control Sample in any/multiple lanes,
Of your requirements:
1. Those features that are currently supported include:
- runs on UNIX
- performes BLAST against local data bases
- displays the results via a WWW interface
- selects significant hits (cut-off by user-defined
criteria)
- re-runs the BLAST in a time-dependent way
2. Those features that are in the current development cycle:
- does vector trimming in a project-specific way
- allows text-based searches of the annotation data
of hits
3. Those features that require development scheduling:
- combines data from both ends of the cDNA (5-prime
and 3-prime sequences)
More information is available on my web site:
http://www.dnatools.com
I am attending a conference in England and will return April 16, 1999.
I can provide more system information and would be happy to discuss
your needs and my software solution when I return.
Thank you,
Jerry Tuneberg
970-689-9268 p
970-226-8723 f
jerryt@dnatools.com
Bernd Weisshaar wrote:
Dear Sequers & BLASTers,we have recently faced the problem that more and more of our our customes
want to do small EST projects of a few hundert to up to 10000 ESTs. The
generation of the primary data works nice, but the data analysis side of
things is a problem.I am looking for software which does the following (hints on partial
solutions also wellcome!):- runs on UNIX
- does vector trimming in a project-specific way
- combines data from both ends of the cDNA (5-prime and 3-prime sequences)
- performes BLAST against local data bases
- displays the results via a WWW interface
- selects significant hits (cut-off by user-defined criteria)
- allows text-based searches of the annotation data of hits
- re-runs the BLAST in a time-dependent wayObviously, the task list can be made longer, but ....
Thanks and best regards, Bernd
_____________________________________________________________________PD Dr. Bernd Weisshaar
MPI fuer Zuechtungsforschung
Carl-von-Linné-Weg 10
50829 Koeln
GermanyTel. office: +49-221-5062 590 Tel. lab: +49-221-5062 311
Fax: +49-221-5062 313
e-mail: weisshaa@mpiz-koeln.mpg.de
WWW-URL: http://www.mpiz-koeln.mpg.de/~weisshaa/BW-info.htm
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