Table 1.
Comparison matrix of popular annotation tools: the first column defines features supported by the respective tools given in column 2–5. Available/not available features are coded as Y or N, respectively. In case of comparable features, explanations/details are given as key words. *Indicates “only via additional programming”.
| Homer | GREAT | ChiPpeakAnno | Goldminer | UROPA | |
|---|---|---|---|---|---|
| Annotation Database | Refseq | UCSC (internal database) | Pre-calculated sets, e.g. “EnsDb.Hsapiens.v75” | All genomic range files | All GTF formatted files |
| Helper script to generate annotation file | assignGenomeAnnotation | N | N | makeGRanges() | UROPAtoGTF-tool |
| Target for distance calculation | TSS only | TSS only | Start/Center/End of selected feature | Overlap | Start/Center/End of selected feature |
| Select feature type in annotation file | N | N | Y | (N)* | Y |
| Limitation on characteristics, e.g. “protein_coding” | N | N | N | (N)* | Y |
| Definition of multiple annotation queries | N | N | N | N | Y |
| Prioritization of queries | N | N | (Y) no exclusive ranking (precedence) | (Y) within gene model context, but not globally | Y |
| Limit results to upstream/downstream of selected features | N | N | N | N | Y |
| Granularity of resulting annotations | N | N | Shows all hits, no aggregation to the best hit | Clear result structure, but single best hit is often missing | All hits, best hits per query, and merged best hits among all queries |
| Parallelization | N | N | N | N | Y |
| Simple customizing (no programming) | N | Y (only in web-based version) | N | N | Y |
| Audience | Bioinformatician/Biologist | Biologist | Bioinformatician | Bioinformatician | Bioinformatician/Biologist |
| Definition of distance cutoff | N | N | Y | N | Y |