Bioinformatics Workshops
Welcome to Dr Dickins's Bioinformatics Class
Pre-requisites
It is useful to have a professional text editor. Unfortunately, Notepad (on Windows) or TextEdit (on MacOS) tend to correct spelling. This is not something we want when handling sequences. In addition, Notepad has a problem displaying newline characters which tend to differ between platforms. This is a pain when viewing FASTA files.
If you are using an NTU PC, I recommend launching an instance of "Notepad++" via NTU's Software Centre (icon on Desktop). If you are using your own computer running Windows you can get it from this link. For those of you with a technical bent, and on any OS, try GitHub's own Atom editor.
Links to Content
Please follow the links below to the appropriate class:
| Workshop # | Workshop Title & Link |
|---|---|
| 1 | BLAST Searching |
| 2 | Sequence Retrieval & Alignment |
| 3 | Genome Browsers |
| Help! | Getting Repeat Data from UCSC |
Improvements
Literature/Guides
I have identified this very useful guide (available from NTU library). This runs through phylogenetic tree construction methods and highlights some issues that are currently under-emphasised in the workshop. These include the ability to rotate around nodes, placement of the root (think about your most distant sequence), the usefulness of bootstrap measures and the common, but important, issue of long-branch attraction (consider your interpretation).
Note that the Simple Phylogeny tool used does not appear to offer bootstrap options and you may wish to try the tools/workflows on phylogeny.fr for this purpose.
Recall also the reference given in my Paralogy lecture:Koonin, E. V. (2005) Orthologs, paralogs, and evolutionary genomics. Annu. Rev. Genet., 39: 309-338.
Alternative Software
The following software could be tried:
- MAFFT (for alignment): click on "Algorithms" for an explanation of its approach.
- Gblocks server: if you wish to avoid phylogeny.fr.