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Geneious for Genomics Analysis

Poorani Subramanian 2020-02-25

BCBB Science Support

Geneious at NIAID

  • Can install through Self-Service app
    • Need to also install the Key Server/K2 Client – this provides the license
  • Technically, if you have K2 Client installed, you can also install newest version of Geneious through Geneious website
  • NIAID has 30 "floating" licenses – 30 people can use simultaneously
    • If you ever notice that the license doesn't work or you get booted, note roughly the time, and email bioinformatics@niaid.nih.gov
    • We can re-evaluate if we need more licenses
  • If you need more computer power than your desktop/laptop allows, please let us know as well.

Geneious online help

Primer Design

  • Geneious uses Primer3 for primer design - v 2.3.7 modified
  • current version of Primer3 is 2.5.0 released Aug 2019
  • NC_007596 2.5.0 released Aug 2019

Design New Primer Pair – other options

  • Design for Sequencing – tile amplicons across a region
  • A mispriming library is a set of sequences (usually repeats) which the primers should not bind to. – Included libs are from Primer3

CRISPR site finder

  • searches for gRNA sites in your selected sequences, and scores them based on on-target sequence features (activity score) and off-target interactions (specificity score).
  • target sequence <= 1000bp

CRISPR Site Finder - activity scoring

  • Activity scoring for Cas9 CRISPR
    • method from Doench et al. (2014): analyzes the one- and two-base features of the gRNA, as well as the GC content, to generate the score. Scores are between 0 and 1, with a higher score denoting higher expected activity.
    • ambiguous bases will not contribute to this score.
    • Not available for Cpf1 Doench et al. (2014):

CRISPR Site Finder - specificity scoring

Switching from Vector NTI

Thanks!