Algorithmen der Sequenzanalyse

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Algorithms in Sequence Analysis 12 - Tree heuristics, splits and ortologs

  • Untertitel   reconstruct phylogenetic tress form sequence data; Calculating tree likelihoods; how to find the ML tree; Tree rearrangements in RAxML; Subtree; Rapid bootstrapping in RAxMl; Looking at trees via their splits; Split Compability; Strict Consensus Trees; L
  • Sprecher   Prof. Dr. Ingo Ebersberge
  • Ort   Biologicum - Bio 3.201
  • Datum   20.07.2017 @ 09:21

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Algorithms in Sequence Analysis 13 Pologemy Reconstruction Part 2

  • Untertitel   phylogenetic trees; The principle of Maximum Parsimony; Fitch algorithm; Distance-based tree reconstruction; Metric; The Four-Point-Condition; Modeling sequence evolution; Tree likelihoods;
  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio 3.201
  • Datum   13.07.2017 @ 09:36

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Protein Binding motifls ChIP-Seq and CLIP-Seq

  • Untertitel   NGS Applications; DNA-Protein Binding Sites; ChIP-Seq; Chip-seq analysis; Chip-seq normalization; Naive scaling unequal datasets; Peak calling; Program algorithm characteristics; Strand specific bimodality; Backround fold change; Noise level; MACS tool; U
  • Sprecher   Dr. Stefan Simm
  • Ort   Biologicum - Bio 3.201
  • Datum   06.07.2017 @ 09:13
  • Beschreibung   Achtung: Video sehr laut

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Modeling biological sequences Coping with finite training data

  • Untertitel   Plan 7 pHMMs; Revisiting the problem of finite size training data; The Problem with small training data at its extremes; Modeling Sequence evolution; Molecular function in the context of biological sequence evolution is a bit problematic
  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - 3.201
  • Datum   29.06.2017 @ 09:27

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Modelle in der Sequenzanalyse (PSSMs, Markov Ketten und (profil-)hidden Markov Modelle

  • Untertitel   Pfam; Modelle können auch zu detailliert sein; Unser Beispiel für die Vorlesung ROX1; Wie Suche ich nun nach Signalsequenzen?; Bindungsstellen-Vorhersage für ROX1; PSSMs; Markov-Ketten; Identifizierung des Viterbi-Pfads erfolgt über Dynamische Programmier
  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio 3.201
  • Datum   22.06.2017 @ 09:23

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High-throughput Sequencing RNA-Seq and Applications

  • Untertitel   NGS Preparation – From total RNA to Fragments; 2nd & 3rd NGS Technologies; Quality, Pre-processing & Mapping; Normalization Approaches; Applications of RNA-Seq; Alternative Splicing; Whole Genome Alternative Splicing Detection; AS Expression Algorithms
  • Sprecher   Dr. Stefan Simm
  • Ort   Biologicum - Bio 3.201
  • Datum   08.06.2017 @ 09:30
  • Beschreibung   Wg. eines Krankheitsfalles konnten die ersten 15 min. leider nicht aufgezeichnet werden, sorry!

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Sequence Alignment

  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio 3.201
  • Datum   01.06.2017 @ 09:15

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Algorithms in Sequence Analysis 5

  • Untertitel   Different approaches to the sequence assembly problem; Genom assembly abstracted to the problem of finding a shortest superstring; Basic concepts of the Brujin graph based assemblers; Considering the size of K; Coverage and Kmer coverage; Kmer; Velvet: Gr
  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio 3.201
  • Datum   18.05.2017 @ 09:17

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Strategies to sequence long DNA molecules: Shotgun sequencing and reference guided sequence assembly

  • Untertitel   Short Read Application; RNA-seq mapping helps building hypotheses concerning gene structure; Short Read Applications; Short Read Alignment; Finding mapping positions is, in principle, very easy!; Indexing; The three phases of Bowtie
  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio 3.201
  • Datum   11.05.2017 @ 09:21

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Algorithms in Sequence Analysis 3

  • Untertitel   Strategies to sequence long DNA molecules; There are two main approaches to the sequence assembly problem; Overlap-Layout-Consensus; Derive Consensus Sequence; Eulerian Cycle Problem; Passing through the edges by following the roman numbers reconstructs t
  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio 3.201
  • Datum   04.05.2017 @ 09:08

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Recording 20170427-09_56_56_658.tar

  • Datum   27.04.2017 @ 09:56
  • Beschreibung   Teil 2

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Recording 20170427-09_45_53_524.tar

  • Datum   27.04.2017 @ 09:45
  • Beschreibung   Teil 1

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Organisatorisches, Am Anfang steht die Sequenz

  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio 3.201
  • Datum   20.04.2017 @ 09:00