GACK (Genomotyping Analysis by Charlie Kim) analysis is used as a microarray-based
genome analysis tool. The software is used within comparative genomics
to differentiate between genes that are present (core genes) or 'absent
or highly divergent genes' (in comparative genomics, genes are never definitively
absent, they are said to be absent or highly divergent).
GACK analysis is free software that was produced by Charlie Kim at Stanford
US (Kim, CC. et al 2002). It uses an algorithm which dynamically
calculates the category a gene should belong to. Many other tools are
available for calculating cut-offs, however, these are often empirically
determined for the classification of genes in a certain category. GACK
is based on dynamically determining the cut-offs for each array at a time.
The current version of the GACK interface is 3.631. The software can
place genes into different categories based upon calculations using an
EPP (Estimated Probability of Presence value). Initially the data loaded
must be in either .pcl or .cdt format (see protocol). The user has options
to generate a log file, histogram data with graphs. The user can also
select for binary or trinary outputs. Binary would generate genes designated
as 1 (present) and -1 (absent or highly divergent). Alternatively, a trinary
selection gives present genes, 'absent or highly divergent genes' and
also marginal genes that cannot definitively be classed in either category.
The elucidation of genes within these categories allows further analysis
to be carried out e.g. clustering analysis on 'absent or highly divergent
To view a basic protocol for GACK, click here.
To view frequently asked questions on GACK, click here.