DNA/Genome Engineering With Geneious

3 Jul 2019, 09:00 → 4 Jul 2019, 15:00 Europe/Berlin

CSBD Seminar Ground Floor (MPI-CBG/CSBD)

Mihail Sarov

What is Geneious?

Geneious is an extremely versatile sequence analysis and manipulation package that covers a wide range of tasks - from routine things like PCR design, cloning, sequence alignments to advanced NGS data processing. It is available to anyone at the MPG  but sadly a lot of people are unaware of it or what it has to offer, which is the reason for this course.

Main advantages of Geneious:

- the ability to store the data on a shared server space, which allows collaborative work on the same file(s) and makes it very simple to keep track of and reuse plasmids, primers etc. within the same lab or to share them with colleagues.
- many of the tools in Geneious are open source algorithms packaged into an easy to use interface, combining simplicity with full control over how your data is handled.
- the software is supported by the MPI-CBG Scientific Computing Facility, and they can develop custom plugins for specialised tasks.

Who is this course intended for:

Students, postdoc and technicians, whose work includes regular cloning, sequence analysis, etc (see below for a full list of topics covered). The course is a basic introduction to Geneious and is not intended for advanced users. Prior knowledge of other sequence analysis software or programming is not required. 

What if I am already using other tool(s) for the same tasks like ApE, SnapGene, MacVector, CLC, GCK etc. etc.?

It is very likely that you will leave them behind, once you see what Geneious has to offer. Don’t worry, you can take your data with you.

Topics covered in the course:

1. Import/Export of data, collaboration using shared server space
2. Annotating sequences from a features library, using BLAST or motif databases
3. PCR primer design, reuse of database stored primers
4. Codon adaptation analysis and optimisation
5. Classic restriction/ligation cloning
6. Gateway cloning
7. Golden gate cloning
8. Gibson assembly and CPEC cloning
9. Genome engineering with CRISPR/Cas
10. Sequence analysis - sequence alignments, SNP mapping
11. Using workflows to automate routine tasks
12. Brief overview of other useful features that will not be covered in the practical exercises: NGS data processing, genome assembly, phylogenetic analyses; custom plugins

 

Minutes collaborative note taking

Slides

• CRISPR.pdf
• gateway.pdf
• Gibson-CPEC.pdf
• goldengate.pdf