From: Uwe Ohler <ohler@informatik.uni-erlangen.de>
Sender: ohler@informatik.uni-erlangen.de
To: mgreese@lbl.gov
Subject: Re: Information on submissions
Date: Fri, 23 Jul 1999 14:33:27 +0200

Hi Martin,


> 1. List of credits (group members) possibly with affiliation, email
> addresses and URLs.

Uwe Ohler
Georg Stemmer
Stefan Harbeck
Heinrich Niemann

Chair for Pattern Recognition (Computer Science V)
University of Erlangen-Nuremberg, Germany
eMail: ohler@informatik.uni-erlangen.de


> 2. A short 3 sentence description of your methods that will be
> published in the tutorial hand outs and displayed during our
> discussion of your techniques (see #3 below).

(You have that already, right?)

> 3. Up to 3 paragraphs more detailed background information about the
> methodology.  (topics to mention:

> A. Training data:

Representative set of promoters, coding, and non-coding sequences of D.
melanogaster
(http://fruitfly.berkeley.edu/pub/genesets)

>         B. Version of program(s).

LME-IMC: Version 1.1 of the Markov Chain Promoter Finder, based on maximum
mutual information (MMI)
estimated interpolated Markov chains (IMC) (see references below)
LME-SSM: Version 2.0 of the Markov Chain Promoter Finder, based on ML
estimated Markov chains for non-promoters
and a 5-state stochastic segment model (SSM) for promoters

>         C. Running time of the program(s).

On a fast PC, roughly 100 bases per second for V2.0, and ~3 times faster
for V1.1 (simpler model structure)

>         D. Fully automatic annotations or manual interactions and if
>         so of what kind.

Fully automatic except a threshold which regulates the total number of
predictions.

>         F. Estimate of time and people needed for complete annotations.

Adaption and evaluation specifically for Drosophila: 1-2 days for 1 person.

> 4. List of References for used tools/methods

@Article{Ohler99:IMC,
  author =       {U.~Ohler and S.~Harbeck and H.~Niemann and E.~N{\"o}th
                  and M.~G.~Reese},
  title =        {{Interpolated Markov chains for eukaryotic promoter
                   recognition}},
  journal =      {Bioinformatics},
  year =         {1999},
  volume =       {15},
  number =       {5},
  pages =        {362--369},
}

@InProceedings{Ohler99:DEO,
  author =       {U.~Ohler and S.~Harbeck and H.~Niemann},
  title =        {Discrimative Estimation of Language Model Classifiers},
  booktitle =    {Proc. EUROSPEECH},
  year =         {1999},
  address =      {Budapest},
  note =         {to appear},
}

> 5. URL(s) of program(s) used; more information about programs/tools
> used (example: accessible over the Web, to download)

hopefully:
http://www5.informatik.uni-erlangen.de/HTML/English/Research/Promoter

Bye,
-- Uwe

--
Dipl.-Inf. Uwe Ohler           eMail:ohler@informatik.uni-erlangen.de
Lehrstuhl f. Mustererkennung   http://www5.informatik.uni-erlangen.de
Universitaet Erlangen-Nuernberg
Martensstr. 3                              Phone:  ++49-9131/852 7826
D-91058 Erlangen (Germany)                    Fax:  ++49-9131/30 3811
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