Algorithmen der Sequenzanalyse

Diese Vorlesung abonnieren (RSS-Feed)
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Of species trees and gene trees

  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio - 1.302 Seminarraum 3
  • Datum   18.07.2019 @ 09:21
  • Beschreibung   RAxML, in-paralog / co-ortholog, speciation events

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Phylogeny Reconstruction II

  • Untertitel   Calculating tree likelihoods, How to find the ML tree, Finding the best tree, Tree rearrangements in RAxML, Optimizing branch lengths, Likelihood cutoff heuristics, How stable is my tree?, Resampling methods, Rapid bootstrapping in RAxML, Modeling rate...
  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio - 1.302 Seminarraum 3
  • Datum   16.07.2019 @ 11:00
  • Beschreibung   ..., Looking at trees via their splits: Consensus Trees

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Gillespie Algorithmen

  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio -1.203 (Hörsaal 2)
  • Datum   04.07.2019 @ 09:21
  • Beschreibung   Rate matrix, event rates, site specific rates, phylogenetic trees, likelihood function

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Models (continued)

  • Untertitel   Posterior state probabilities, Forward-Algorithmus, Profil Hidden Markov Modelle, PLAN7 pHMMs, Modellierung biologischer Sequenzen, Problem begrenzter Trainingsdaten, Dirichlet-Dichten / -Verteilungen, Wofür stehen die 9 Komponenten?
  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio - 1.302 Seminarraum 3
  • Datum   02.07.2019 @ 11:00

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Viterbi-Algorithmus / PSSMs

  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio - 1.201 Seminarraum 1
  • Datum   13.06.2019 @ 10:10
  • Beschreibung   Part II: Pseudocounts, HMM, Zustandspfad

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Consistency based alignment strategies (T-COFFEE) / PSSM

  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio - 1.201 Seminarraum 1
  • Datum   13.06.2019 @ 09:18
  • Beschreibung   Part I

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Sequence Alignment

  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio - 1.201 Seminarraum 1
  • Datum   06.06.2019 @ 09:15
  • Beschreibung   Needleman-Wunsch, Smith-Waterman, MSA, Sum of Pairs Score, Progressive alignment strategy, ClustalW, MUSCLE

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Splice-aware alignment for alternative splicing

  • Sprecher   Stefan Simm
  • Ort   Biologicum - Bio -1.203 (Hörsaal 2)
  • Datum   23.05.2019 @ 10:32

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High-throughput Sequencing RNA-Seq and Applications

  • Sprecher   Stefan SImm
  • Ort   Biologicum - Bio -1.203 (Hörsaal 2)
  • Datum   23.05.2019 @ 09:15
  • Beschreibung   NGS Workflow, rRNA depletion, Random hexamer priming, UMI

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Next gen map / Burrows-Wheeler Transform

  • Sprecher   Stefan Simm
  • Ort   Biologicum - Bio - 1.201 Seminarraum 1
  • Datum   16.05.2019 @ 10:33
  • Beschreibung   Part II

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Mapping on reference genomes

  • Sprecher   Stefan Simm
  • Ort   Biologicum - Bio - 1.201 Seminarraum 1
  • Datum   16.05.2019 @ 09:13
  • Beschreibung   Part I: MAQ, Bowtie, NextGenMap, Suffix tree, Burrows Wheller

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The assembly problem...

  • Untertitel   Genome assembly, Different approaches to sequence assembly problem, Finding shortest superstring, de Bruijn graph based assemblers, Kmer coverage, Short read assembly with Velvet, Velvet: Error removal: Tips/Bubbles/Erroneous Connections (Chimera problem)
  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio - 1.302 Seminarraum 3
  • Datum   14.05.2019 @ 11:00
  • Beschreibung   ..., Molekularbiologischer Hintergrund, The problem with repeats: Breadcrumb algorithm

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De novo genome assembly II

  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio - 1.201 Seminarraum 1
  • Datum   02.05.2019 @ 10:44
  • Beschreibung   Hamiltonian and Eulerian cycle, De Bruijn graph, K

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De novo genome assembly I

  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio - 1.201 Seminarraum 1
  • Datum   02.05.2019 @ 09:25
  • Beschreibung   Contigs, Scaffolding, N50 size, Kmer assemblies, CAP3

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High Troughput DNA Sequencing

  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio -1.203 (Hörsaal 2)
  • Datum   25.04.2019 @ 09:15
  • Beschreibung   Illumina, Sanger, Nanopore

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Einführung / Biologische Grundlagen

  • Sprecher   Prof. Dr. Ingo Ebersberger
  • Ort   Biologicum - Bio 3.201
  • Datum   18.04.2019 @ 09:15