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
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;
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
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
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!
Sequence Alignment
Sprecher Prof. Dr. Ingo Ebersberger
Ort Biologicum - Bio 3.201
Datum 01.06.2017 @ 09:15
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
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
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
