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:
Location = 32; Scale = 5.5

Logodds score:

Logodds score:






Background

Cumulative Distribution Function:
Location = 23; Scale = 4.8

a = 1.339e12
b = 2.778e13
c = 45.843

a = 4.46e4
b = 9.125e5
c = 26.929


Stability (logodds)

Stable

1.6

1.37

0.63




Unstable

2.2

3.624

3.17


Nucleus conservation (logodds)

Conserved

3

7.63





Nonconserved

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 deepseq 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, logodds 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 logodds 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:10.1186/1471216412108
