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Table 1 Cutoffs for individual tools at different global confidence levels

From: Structured RNAs and synteny regions in the pig genome

Comp. strategy

High

Medium

Low

BLAST

95% id 95% length

92.5% id 92.5% length

90% id 90% length

Infernal

BLAST E=1e-3

BLAST E=0.1

No BLAST filter

 

Infernal E=1e-3

Infernal E=1e-3

Infernal E=1e-3

Infernal miRNA

Not applied

BLAST E=1e-3

BLAST E=0.1

  

Infernal E=1e-9

Infernal E=1e-6

tRNAscan-SE

High

High

As is

RNAmmer

As is

As is

As is

snoStrip

As is

As is

As is

miRDeep

Hand cleaned

As is

As is

  1. The results from the individual tools are merged at 3 different cutoff levels: high, medium and low. This table shows the correspondence between the cutoff levels of the merged annotation and those of the tools. For each computational (comp) strategy, we define these levels. Note that Infernal screen have been divided into Infernal (without miRNAs) and Infernal miRNA which is only for miRNA families. The Infernal results were filtered by the family specific gathering scores as well. For As is, we refer to the programs default values for the respective versions (see the Methods section for version numbers) without subsequent cleaning.