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Table 1 Operation modes of SLALOM. Each input is parsed twice, so that each annotation is at one point the query and the subject, respectively

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

Mode Description
Count modes (mutually exclusive, collectively exhaustive)
 Symbol-resolved While calculating symbol-wise statistics, classify symbols to either present or absent in the query annotation. Calculate site-wise statistics according to the overlap logic. This is the default mode.
 Gross While calculating symbol-wise statistics, count each symbol gross, i.e., as many times as it occurs in all sites from the query annotation. Calculate site-wise statistics according to the overlap logic.
 Enrichment While calculating symbol-wise statistics, classify symbols to either enriched or non-enriched (including completely absent) in the query annotation based on the user-provided threshold on the number of occurrences. Do not calculate site-wise statistics.
Comparison modes (mutually exclusive, collectively exhaustive)
 Equal Treat the two input annotations as equal. Calculate only symmetric (not influenced by swapping) performance measures.
 Benchmarking Treat the first input annotation as the benchmark; treat the second one as a prediction. Calculate both symmetric and non-symmetric performance measures.