Material for the master course Computer Applications in the Biosciences

Lectures

Lecture 01 – Historical Background: Informatics, Computers and Operating Systems
Lecture 02 – The Operating System GNU/Linux
Lecture 03 – Literature Retrieval and Submission of Manuscripts
Lecture 04 – Searching Bioinformatics Databases: Pairwise Alignment Algorithms
Lecture 05 – Molecular Phylogeny: Trees and Multiple Alignments
Lecture 06 – Molecular Phylogeny: Parsimony and Heuristic Tree Search
Lecture 07 – Molecular Phylogeny: Evolutionary Models, Distances and Maximum Likelihood
Lecture 08 – Molecular Phylogeny: Bayesian Analysis and Systematic Biases in Phylogenetic Inferences
Lecture 09 – Protein-Coding Genes: Codon Usage Biases
Lecture 10 – Proteins: Database Searches, Phylogenies and Supermatrices
Lecture 11 – Protein Structure Prediction
Lecture 12 – Genomics
Lecture 13 – Proteomics and Systems Biology

Topic 1 – The apicoplast
Topic 2 – DNA barcoding in diatoms
Topic 3 – Profile-HMMs for prediction of transmembrane helices and signal peptides
Topic 4 – Scaffolding of metagenomes
Topic 5 – Base-calling in next generation sequencing
Topic 6 – Phylogenetic position of Paulinella chromatophora
Topic 7 – Pitfalls of phylogenetic methods
Topic 8 – Minicircles in dinoflagellate plastids

Assembly, editing and analysis of sequences: The Staden Package
Searching for (putatively) homologous sequences: The BLAST suite and HMMER3
Multiple interactive sequence alignment: SeaView
Selecting the best-fitting evolutionary models for protein phylogenies: ProtTest
Maximum likelihood analysis: RAxML and PhyML (diverse versions)
Bayesian analysis: MrBayes (recent and archived versions)
Using several processors at once for an analysis: MPICH2 (also precompiled in GNU/Linux distributions)
A large collection of links to phylogeny software by Joe Felsenstein: Phylogeny Programs
An assembler for small genomes: MIRA
Codon usage analysis: CodonW