Additional file 3 of Widespread, focal copy number variations (CNV) and whole chromosome aneuploidies in Trypanosoma cruzi strains revealed by array comparative genomic hybridization

Additional file 3:A java-based executable file for viewing all of the CGH array data from this study. The CGH data were visualized and explored using 'CGH_Viewer,' which was written in the Java programming language. Additional file 2 is a Windows executable (.exe) that will install the CGH_Viewer, along with Java if it is not detected, on the target computer. The CGH_Viewer takes as input the mapping of probes from the microarray to the assembled chromosomes of T. cruzi as well as the results of 1 or more experiments between 2 strains. The probe-to-chromosome mapping file and the 16 experimental files are provided in the "Data" sub-folder. The results (dot plots of log2 ratios) of multiple chromosomes and multiple experiments may be viewed simultaneously. Zooming on an area of interest on a chromosome will show the same region across all experiments. The data can be filtered based on 1) the haplotype of sequence from which the probes were designed as well, 2) the ID or name of the sequence from which the probe was designed, 3) by raw intensity of the probe (a quality measurement), or 4) a sub-region of a chromosome. For additional information, see the provided documentation in the CGH_Viewer program folder (c:\Program Files\CGH_Viewer\). (EXE 92 MB)