Table 1

List of miRDeep parameters estimated for plant specific miRNAs.

Feature

Original parameters of miRDeep

Plant specific (monocot)

Dicot specific (if any)


MFE

Known

Cumulative Distribution Function: <a onClick="popup('http://www.biomedcentral.com/1471-2164/12/108/mathml/M12','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/12/108/mathml/M12">View MathML</a>

Location = 32; Scale = 5.5

Log-odds score: <a onClick="popup('http://www.biomedcentral.com/1471-2164/12/108/mathml/M13','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/12/108/mathml/M13">View MathML</a>

Log-odds score:<a onClick="popup('http://www.biomedcentral.com/1471-2164/12/108/mathml/M13','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/12/108/mathml/M13">View MathML</a>


Background

Cumulative Distribution Function: <a onClick="popup('http://www.biomedcentral.com/1471-2164/12/108/mathml/M12','MathML',630,470);return false;" target="_blank" href="http://www.biomedcentral.com/1471-2164/12/108/mathml/M12">View MathML</a>

Location = 23; Scale = 4.8

a = 1.339e-12

b = 2.778e-13

c = 45.843

a = 4.46e-4

b = 9.125e-5

c = 26.929


Stability (log-odds)

Stable

1.6

1.37

0.63


Unstable

-2.2

-3.624

-3.17


Nucleus conservation (log-odds)

Conserved

3

7.63


Non-conserved

-0.6

-1.17


Excision length

140 nt

300 nt


Paired

Total

≥14

≥15 nt


Unpaired

Total

NA

≤5 nt


Consecutive unpaired

NA

≤3 nt


Bulge

Total

could be as high as 5 nt #

≤2 nt


Maximum multiple hits of deep-seq read

5

20


The cumulative distribution of MFE of known and background precursors, in miRDeep algorithm, are represented by Gumbel distribution functions, where F(x) is the cumulative frequency of MFE less than or equal to variable x, and location is used for mean centering the distribution of MFE. On the other hand, in the parameterized algorithm, log-odds of MFE were directly obtained from the distributions of real and background precursors, and then represented by a modified sigmoid function where f(x) denotes log-odds of a given normalized MFE. #The size of bulge was estimated based on allowed difference between length of mature and star sequences in miRDeep. The bulges often appear when one of the duplex sequences has additional bases than its counterpart.

Thakur et al. BMC Genomics 2011 12:108   doi:10.1186/1471-2164-12-108

Open Data