Bioinformatics workshop scripts

Please choose the appropriate set, either undergraduate, or postgraduate.

Undergraduate Bioinformatics workshops

These are the scripts for the first two Bioinformatics workshops (for reference, I'll give out paper copies in the workshops), and the question for the third.

Workshop 1: Extracting sequences from databases

Workshop 2: Sequence alignment and phylogenetic trees

Example unaligned nucleotide sequence file for workshop 2 mynuc.fasta

Corresponding protein sequences aligned with ClustalW2 myprotaln.fasta

Workshop 3: Analysis of sequence similarity

Postgraduate Bioinformatics workshops

These are the scripts for workshops I give to new postgraduate students but can be used for reference by anyone else!

  • Workshop 1: Sequence analysis - what can I find out from my sequence?

  • Translating a DNA sequence into protein, using BLAST and PSI-BLAST to find related sequences and structures. Visualising structures using JMol.

  • Workshop 2 : Multiple sequence alignments and phylogenetic trees

  • Use of ENTREZ to obtain sequences by function, use of CLUSTALW to align these sequences, use of JalView, BOXSHADE and ESPript to display sequence alignments, making nucleotide sequence alignments and finally phylogenetic trees using PHYLO_WIN.

  • Workshop 3: Modeling protein structure from sequence

  • Use of Swiss-Model for structure modelling, use of PROCHECK for model validation and DaliLite for model comparison.

    Revision session 

    Revisiting some of the above methods.