Balony: a software package for analysis of data generated by synthetic genetic array experiments

BMC Bioinformatics. 2013 Dec 4;14:354. doi: 10.1186/1471-2105-14-354.


Background: Synthetic Genetic Array (SGA) analysis is a procedure which has been developed to allow the systematic examination of large numbers of double mutants in the yeast Saccharomyces cerevisiae. The aim of these experiments is to identify genetic interactions between pairs of genes. These experiments generate a number of images of ordered arrays of yeast colonies which must be analyzed in order to quantify the extent of the genetic interactions. We have designed software that is able to analyze virtually any image of regularly arrayed colonies and allows the user significant flexibility over the analysis procedure.

Results: "Balony" is freely available software which enables the extraction of quantitative data from array-based genetic screens. The program follows a multi-step process, beginning with the optional preparation of plate images from single or composite images. Next, the colonies are identified on a plate and the pixel area of each is measured. This is followed by a scoring module which normalizes data and pairs control and experimental data files. The final step is analysis of the scored data, where the strength and reproducibility of genetic interactions can be visualized and cross-referenced with information on each gene to provide biological insights into the results of the screen.

Conclusions: Analysis of SGA screens with Balony can be either automated or highly interactive, enabling the user to customize the process to their specific needs. Quantitative data can be extracted at each stage for external analysis if required. Beyond SGA, this software can be used for analyzing many types of plate-based high-throughput screens.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Colony Count, Microbial / instrumentation
  • Colony Count, Microbial / methods
  • Fungal Proteins / biosynthesis
  • Fungal Proteins / genetics
  • Genes, Fungal*
  • Genome-Wide Association Study / instrumentation
  • Genome-Wide Association Study / methods*
  • High-Throughput Screening Assays / instrumentation
  • High-Throughput Screening Assays / methods*
  • Image Processing, Computer-Assisted / instrumentation
  • Image Processing, Computer-Assisted / methods*
  • Internet
  • Mutation / genetics
  • Oligonucleotide Array Sequence Analysis / methods*
  • Saccharomyces cerevisiae / cytology
  • Saccharomyces cerevisiae / genetics
  • Saccharomyces cerevisiae / isolation & purification
  • Software* / trends
  • User-Computer Interface


  • Fungal Proteins