Table 1 Comparison to other tools Itemized comparison of the features of Caryoscope ([15]), CGHAnalyzer ([12],[22]) and SeeCGH ([11],[23]).
From: Caryoscope: An Open Source Java application for viewing microarray data in a genomic context
| Â | Caryoscope | CGHAnalyzer | SeeGH |
|---|---|---|---|
Platform | Java (runs on any popular platform) | Java (runs on any popular platform) | Microsoft Windows |
Application availability | Unlimited use; no signup | Unlimited use with signup | Free with signup for academics |
Installation process | Install Java; run application directly from Web | Install Java; install application | Install MySQL; install application; configure database tables |
Input file formats | Single input file; spreadsheet compatible text or General Feature Format (GFF) | Multi-component input; text-based input formats | Text-based input formats |
Internal data format | Text file | Text file or database | MySQL database |
Source code availability | Free download | Download with signup | Not available |
Source code license | Open Source | Unknown | N/A |
Internal code dependencies | All Open Source | Depends on some commercial software | N/A |
Superimposed karyotype plot | No | Yes | Yes |
Informational summary for each feature | Yes, configurable in application settings | Yes, fixed tabular format | Yes, fixed tabular format |
Web link from each feature | Yes, configurable in application settings | Yes, fixed Ensembl or GoldenPath links | No |
Data points in genome coordinates | Yes | Yes | Yes |
Data points in linear order | No | Yes | No |
Simultaneous display of multiple experiments | No | Yes | No |
Zoomable display | Yes | No | Yes |
Part of a more complete analysis framework | No | Yes (TIGR MeV) | No |
Built-in data point filtering | No | No | Yes |
Whole-genome view | Linear chromosomes | Concentric circles representing chromosomes | Linear chromosomes |
Generate graphics from command line | Yes | No | No |