Skip to main content

Table 6 Overview of the functionality of the discussed tools for comprehensive annotation comparisons

From: SLALOM, a flexible method for the identification and statistical analysis of overlapping continuous sequence elements in sequence- and time-series data

   SLALOM (v2.1.4) Bioconductor (version 10/2017) bedtools (v2.25.0) BEACON (as in [8])
Overlap sufficiency criteria to match Symbol count yes yes no no
Length share yes no yes yes
Order yes yes no no
Enrichment yes yes yes no
Match by proximity without overlap yes yes yes no
Application principle of the overlap criteria Shortest yes no no yes
Longest yes no no no
Current yes yes yes no
Patched yes yes no no
Resolving overlaps within single annotation Merge yes yes yes no
Disjoin no yes no no
Leave one yes no no no
By enrichment yes no yes no
Residue-wise statistics Symbol-resolved yes yes no no
Gross yes no no no
Site-wise statistics yes yes yes yes
Performance measures yes no no no
Jaccard statistics no yes yes no
Sequence grouping yes yes yes yes
Combining annotations yes yes yes no
Time series processing yes no no no