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GACK Overview


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 genes'.

To view a basic protocol for GACK, click here.

To view frequently asked questions on GACK, click here.