Authors: Aidan Budd or Bruno Gaeta
Slides used for teaching an introduction to phylogenies and MSAs in the context of phylogenies for the first day of a two-day course on MSAs at Cambridge University, in the UK, in December 2013. Course taught together with Holger Dinkel and Terri Attwood.
Keywords: Molecular evolution, Multiple sequence alignment, Phylogenetics, Protein sequence analysis, Sequence alignment
Lab 3 in a series of labs given as part of a "bioinformatics for biologists" course targeted at 2nd/3rd year undergraduates and focusing on informed use of tools. Some instructions are specific to our local computer lab setup but overall the content should be adaptable. Note that because some of...
Keywords: Blast, Hmmer, Interpro, Multiple sequence alignment, Similarity searching
This is lab 4 in a series of labs given as part of an undergraduate "Bioinformatics for biologists" course delivered to 2nd and 3rd year biology and bioinformatics undergraduate students, as part of a course focusing on using bioinformatics tools. Some instructions in it are specific to our lab...
Keywords: Clustalw, Multiple sequence alignment, Phylip, Phylogeny
This is lab 2 in a series of labs developed as part of a "bioinformatics for biology undergraduates" course and targeted at 2nd and 3rd year undergraduates. It is meant to be easily assessible. The lab includes some instructions that are specific to our computer lab environment but the content of...
Keywords: Dotmatrix plots, Scoring matrices, Sequence alignment
A presentation given as part of the Basic Evolution Workshop, a trans-African virtual training course (described in this BioEssays article PMID: 21312200; the course wiki is here http://molecevol10.wikispaces.com/). Introduces concepts of splits, consensus trees, consensus networks, describes...
Keywords: Bootstrap, Consensus trees, Phylogenetic splits, Phylogenetics
An introduction to multiple sequence alignments (MSAs) for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on describing: the "anatomy" of a sequence alignment; two alternative interpretations of...
Keywords: Multiple sequence analysis, Protein structure, Sequence analysis
An introduction to bioinformatics for bench biologists delivered as part of the EMBL Australia Masterclass on Protein Sequence Analysis http://oz-masterclass.wikispaces.com/ . Focuses on using UniProt to explore different reasons why information inferred by "direct assay" and "prediction" could...
Keywords: Introduction bioinformatics
Content for a one-day course delivered in April 2013 at the University of Cambridge, together with Sarah Parks, Cilia Antoniou, and Adrian Friday.
Uses examples taken from several published papers to explore some of the assumptions and concepts we use when presenting and interpreting phylogenetic...
Keywords: Molecular evolution, Phylogenetics