Vorbesprechung Seminar Biomedical Informatics

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1 Vorbesprechung Martin Dugas und Xiaoyi Jiang Institut für Informatik Sommersemester 2016

2 Organisation Vorlage: Englischsprachige Publikation Vortrag: ca. 30min + 15min Diskussion, Blockseminar Anfang/Mitte Juni Seminararbeit: ca. 15 Seiten 8 CP (Master Informatik oder Mathematik)

3 Von der DNA zur Sequenz DNA extraction Fragmentation GATTCGATAGATC GTCTCTCAGCAT TTAGATCGTCGATA CACTAGCGATCATCG GATCAGCTACTAGCTA Preparation and sequencing Alignment to reference

4 Themen 4 Themengebiete, 12 Themen rund um DNA-Sequenzen

5 1. Alignment von DNA-Sequenzen Herausforderung: Referenzsequenz ist sehr lang Sehr viele kurze Sequenzen Sequenzierungsfehler & Mutationen

6 1. Alignment von DNA-Sequenzen - Paper 1 A space-efficient algorithm for local similarities Huang X et al., Computer Applications in the Biosciences MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping Lee WP et al., PLOS One Fast and accurate short read alignment with Burrows-Wheeler transform Heng Li and Richard Durbin, Bioinformatics 2009

7 1. Alignment von DNA-Sequenzen - Paper 4 Stampy: A statistical algorithm for sensitive and fast mapping of Illumina sequence reads Gerton Lunter and Martin Goodson, Genome Research Optimal seed solver: optimizing seed selection in read mapping Xin H et al., Bioinformatics 2016

8 2. DNA-Mutationen

9 2. DNA-Mutationen - Paper 6 Unified representation of genetic variants Tan A et al., Bioinformatics BreaKmer: detection of structural variation in targeted massively parallel sequencing data using kmers Abo RP et al., Nucleic Acids Research 2014 & BLAT - The BLAST-Like Alignment Tool Kent WJ, Genome Research 2011

10 2. DNA-Mutationen - Paper 8 Learning the parts of objects by non-negative matrix factorization Lee DD and Seung HS, Nature 1999 Mit Anwendung in: Deciphering Signatures of Mutational Processes Operative in Human Cancer Alexandrov LB et al., Cell Reports 2013

11 3. Indizierung und Komprimierung großer Datensätze (Hunderte) Millionen von Sequenzen Effizienter Zugriff? Komprimierung? Visualisierung? Overlap zwischen Sequenzen? R-Trees, Nested Containment Lists

12 3. Indizierung und Komprimierung großer Datensätze - Paper 9 R-Trees: A dynamic index structure for spatial searching Guttman A, Proceedings of the 1984 ACM SIGMOD international conference on Management of data Mit Anwendung in: BigWig and BigBed: enabling browsing of large distributed datasets Kent WJ et al., Bioinformatics Nested Containment List: a new algorithm for accelerating interval query of genome alignment and interval databases Alekseyenko AV et al., Bioinformatics 2007

13 4. DNA-Motive Suche und Analyse von kurzen, prägnanten, wiederkehrenden DNA-Sequenzen:

14 4. DNA-Motive - Paper 11 Detection of generic spaced motifs using submotif pattern mining Wijava E et al., Bioinformatics MotifVoter: a novel ensemble method for fine-grained integration of generic motif finders Wijava E et al., Bioinformatics 2008