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

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

		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
Residue-wise statistics	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

ISSN: 1471-2105