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A maximum expectation value of 0.1 was employed as a threshold for peptide identifications.
The maximum expectation value was set to 10-3, and a maximum of 25 alignments were reported per hit.
Although likely to exclude a number of bona fide targets, we used a maximum expectation value threshold of two in order to minimise false-positives.
Because the chip covers 31 099 genes, the maximum expectation value of false positives for each comparison is 3.1 (=31 099 × 0.01 x 0.01).
The maximum expectation value was set to 10-5, the minimum alignment length was set to 50 bases, and the minimum percentage identity was set to 50%.
We set the maximum expectation value in BLASTN searches to be e = 10-4 to recover hits that are biologically significant.
Similar(46)
The sensitivity and specificity of these tools, however, crucially depend on parameters such as seed sizes or maximum expectation values.
Acceptance criteria for the reported results were as follows: minimal scores for proteins and peptides were 22 and 15, respectively, and maximum expectation values for proteins and peptides were 0.05 and 0.1, respectively.
We found that there was near-complete overlap between the psRNATarget predictions and those from TargetFinder and the UEA toolkit tool but with fewer predicted targets using the maximum expectation values of two.
Default BLASTX parameters were used including a maximum expectation (E -value of 10.
Maximum TPR values were obtained at the following threshold: psRNATarget: 5 (Maximum expectation), Tapirfasta: 10 (Score), Tapirhybrid: 10 (Score), psRobot: 5 (Penalty score threshold), Target_Prediction: 4 (Penalty score), Targetfinder: 6.5 (Prediction Score), Target-align: 110 (Maximum Score), p-TAREF: 4 (SVR score), RNAhybrid: 1 (p-value).
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