A rudimentary home page to give access to workshop scripts...(Bath only)

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 Rasmol.

  • 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

    • Translation of DNA to protein sequence, use of BLAST for clues to function, use of Swiss-Model and Phyre for structure modelling, use of PROCHECK for model validation and DaliLite for model comparison.

  • Workshop 4: A sequencing project under GCG

    • Use of the bioinformatics package GCG, available on the 4S bioinformatics computer (elf), to join sequenced fragments together to a complete gene. Also uses ENTREZ as in workshop 2, and illustrates finchtv. The GCG manual can be found here.

    Revision session 

    Revisiting some of the above methods including use of Swiss-Model.