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 |