In dieser Veranstaltung wird in Vorträgen über aktuelle Themen aus der Forschung der Arbeitsgruppe Genominformatik berichtet.
Datum | Referent | Titel |
---|---|---|
23.10.2003 | Jomuna V. Choudhuri | GenAlyzer - Overview and Biological Applications |
30.10.2003 | diverse | RNA WORKSHOP |
6.11.2003 | Jens Stoye | On Genomic Distances |
13.11.2003 | Claudia Fried | Footprinting: trailing conserved noncoding sequences in the genome |
20.11.2003 | Ferdinando Cicalese | Threshold Group Testing |
27.11.2003 | Thomas Schmidt | Finding all gene clusters in 2 sequences |
4.12.2003 | - | - |
11.12.2003 | Klaus Schürmann | A fast construction algorithm for suffix arrays |
18.12.2003 | Manuel Scholz | Challenges in Mobile Ad Hoc Networks |
25.12.2003 | X-MAS | - |
1.1.2004 | NEW YEAR | - |
8.1.2004 | Zsuzsanna Liptak | Finding submasses in weighted sequences with FFT |
15.1.2004 | Constantin Bannert | Introduction to PASSTA |
22.1.2004 | Patrick May | PTGL - Protein Topology Graph Library |
29.1.2004 | Sebastian Böcker | Weighted Sequencing from Compomers and beyond... |
5.2.2004 | Michael Spitzer | RiPE: Sampling low-conserved regions for homology-search based tree reconstruction |
12.2.2004 | Michael Kaltenbach | ? |
19.2.2004 | Rileen Sinha | ? |
Kim Rasmussen | ? | |
26.2.2004 | Gregor Obernosterer | Identifying local stable sRNA structures for genome wide surveys |
Thomas Schmidt | ? |
Abstract
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The classical group testing problem is described as follows.
In a set U of n elements, p elements are "positive" and the other n-p
are "negative". A group test consists in asking whether a specified
subset S of U contains at least one of the positive elements. The goal is
to identify the set P of all positive elements by using the least
possible number of group tests.
Group testing is of interest in chemical and biological testing,
DNA mapping, and also in several computer science applications.
We introduce a natural generalization of the group
testing problem: A test gives a positive (negative) answer if the pool
contains at least $u$ (at most $l$) positive elements, and an arbitrary
answer if the number of positive elements is between these fixed
thresholds $l$ and $u$.
We show that the positive elements can be determined up to a constant
number
of miscalssifications, bounded by the gap between the threeesholds.
This is in a sense the best possible outcome. We also study the
number of tests needed to achieve this goal.
We show that in special cases Threshold Group Testing can be
as efficient as Classical Group Testing .
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Title:
"Finding all gene clusters in 2 sequences"
Speaker: Thomas Schmidt
27.11.2003, 16:00 c.t., V4-106
Abstract
--------
A popular approach in comparative genomics is to locate groups or clusters
of orthologous genes in multiple genomes and to postulate functional
association between the genes contained in such clusters. To this end,
genomes are often represented as permutations of their genes and common
intervals, i.e., intervals containing the same set of genes, are interpreted
as gene clusters. A disadvantage of modelling genomes as permutations is
that paralogous copies of the same gene inside one genome can not be
modelled.
In the talk I consider a slightly modified model that allows paralogs,
simply by representing genomes as sequences rather than permutations of
genes. I will sketch a simple algorithm that finds all common intervals of
two genomes
in O(n²) time using O(n²) space and afterwards I will show, more complicated
algorithm runs in O(n²) time and uses only linear space.
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Title:
"Challenges in Mobile Ad Hoc Networks"
Speaker: Manuel Scholz
17.12.2003, 16:00 c.t., V4-106
Abstract
--------
The aspect of mobility has gained much attention in today's research in
computer science. Especially mobile ad hoc networks are the focus of
many research groups. This talk will give a short introduction and
survey of the possibilities and the challenges of mobile ad hoc
networks. Furthermore it will introduce patterns of cooperation among
the network clients and will describe the problem of data dissemination
inside these networks in detail.
--------
Title:
"PTGL - Protein Topology Graph Library"
Speaker: Patrick May
22.01.2004, 16:00 c.t., V4-106
Abstract
--------
The experimental exploration of protein structures is a basic topic of post-genomic research. Therefore, the theoretical analysis and description of protein structures to search for similar protein structures became more and more important. PTGL is a database for protein topologies. The arrangements of secondary structure elements (SSEs) to form motifs and domains in protein structures opens the possibility of their topological description. Topological representations of protein structures are based on sequences of its SSEs, i.e., helices and strands. At this description level protein topologies are defined as undirected labelled graphs. The simplest representation of protein topology are schematic diagrams of protein folds illustrating the SSEs and their spatial neighbourhood. We present a mathematically unique linear notation with a new type of schematic representation, which we have implemented in PTGL combined with an online search tool for data interrogation by sequence similarity and keyword queries.
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Title:
"RiPE: Sampling low-conserved regions for homology-search based tree
reconstruction"
Speaker: Michael Spitzer
05.02.2004, 16:00 c.t., V4-106
Abstract
--------
The homology search stage of RiPE (Retrieval induced Phylogeny
Environment) has been significantly improved by enhanced sampling of
low-conserved regions.
This is done by introducing an additional iteration searching for low-
conserved regions only and incorporating the results into the search
profile. The resulting homologous sequence fragments are larger,
resulting in a better supported and more complete tree.
Secondly, the isoform recognition is improved by using a trained
support vector machine instead of fixed thresholds.
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