Invited Session Mon.1.H 2033

Monday, 10:30 - 12:00 h, Room: H 2033

Cluster 12: Life sciences & healthcare [...]

Computational genomics

 

Chair: Alexander Schönhuth

 

 

Monday, 10:30 - 10:55 h, Room: H 2033, Talk 1

Hugues Richard
Fiona: Automatic correction of sequencing errors in genome sequencing experiments

Coauthors: Manuel Holgrewe, Marcel H. Schulz, David Weese

 

Abstract:
Next generation sequencing technologies can produce a large amount of artifacts. These artifacts are in general limited to one or a few positions, like base substitution or short insertions/deletions. In this context, automatic read error correction is an important step, as it allows to improve the performance of the downstream analysis tasks, such as genome assembly or SNP calling. However most of the proposed methods until now suffer from at least one of the following drawbacks: multiple parameters to set, large memory consumption, or no detection of indels.
We propose a new standalone read error correction method, Fiona, based on suffix trees and which support all type of corrections for any next generation sequencing platform.
Fiona is provided with an efficient implementation in the Seqan library with very small memory consumption that can be run on inexpensive hardware, but also supports multi-core parallelization if available.
When assessing the accuracy of Fiona over an extensive set of conditions it always performed better than all other suffix tree based methods.

 

 

Monday, 11:00 - 11:25 h, Room: H 2033, Talk 2

Marianna D'Addario
DNA sequence design

Coauthor: Sven Rahmann

 

Abstract:
One aim of DNA nanotechnology is to design oligonucleotides (oligos) for the self assembly of complex nanostructures, such as 4x4 tiles.
The principle of DNA self assembly is the q-uniqueness or dissimilarity of oligos that ensures the formation of the desired nanostructure.
To construct a set of q-unique oligos, three rules must be observed: First, every subsequence of length q (q-gram) occurs at most once. Second, if a q-gram occurs, then its reverse complement does not and vice versa. Third, self complementary q-grams do not occur at all.
To generate a DNA sequence, a De Bruijn Graph over the alphabet {A, C, G, T} can be used, where the edges are labeled with all q-grams and the nodes with all (q-1)-grams.
The nodes represent the common overlaps between two successive q-grams.
With an ILP it is possible to find a longest q-unique sequence (a longest path in the graph) by maximizing the number of chosen edges without violating the rules.
This sequence can then be divided into several sequences to form a q-unique set of oligos.
Different additional constraints can be specified.

 

 

Monday, 11:30 - 11:55 h, Room: H 2033, Talk 3

Iman Hajirasouliha
Next-generation sequence characterization of complex genome structural variation.

Coauthors: Can Alkan, Ee. Eichler, F. Hach, F. Hormozdiari, Sc. Sahinalp

 

Abstract:
Structural variation, in the broadest sense, is defined as the genomic changes among individuals that are not single nucleotide variants. Rapid computational methods are needed to comprehensively detect and characterize specific classes of structural variation using next-gen sequencing technology. We have developed a suite of combinatorial optimization algorithms focused on the characterization of structural variants that have been more difficult to assay different forms of genomic structural variation. I will present our algorithms and a summary of our results of 9 high-coverage human genomes regarding these particular classes of structural variation compared to other datasets. In particular, I will also summarize our read-depth analysis of 159 low-coverage human genomes for copy number variation of duplicated genes. The algorithms we have developed will provide a much needed step towards a highly reliable and comprehensive structural variation discovery framework, which, in turn will enable genomics researchers to better understand the variations in the genomes of newly sequenced human individuals including patient genomes.

 

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