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DOT_RNAfinder.cfg
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#
# This file is used by RNAfinder to allow it to run erpin in order
# to identify RNA in genome.
#
# Its format is a list of entry, each entry must start by 'Name = block_name'.
# Each entry is composed of block item.
# Each block begins with 'Item' and ends with 'EndItem'.
#
# Each Item is composed by diferrent fields, some are mandatory others are optional.
#
# Each field must have the following format :
# field_name = Field_value
# field_comment = Comment_value
# order : order used for run program.
# ToFus : 0 if models not need to be merged else 1.
#
# Mandatory fields :
#
# comment : comment about model.
# erpin_arg : list of erpin argument.
# cutoff : cutoff for erpin.
# model_file : file name of the model erpin.
#
#
# Optional fields :
#
# label : used for certain RNA like introns, in order to differentiate RNA
# comment : comments about the model, will be display in Usage
# pos_ac : anticodon position in secondary structure used by erpin
# module : number of modules separated by a comma is used to select the results of erpin,
# when different models are used to define different parts of the same RNA.
# to_comment : 1 if AnnotPair for Mfannot need to be in comment
#
# This file is parsed by the perl class PirObject::RNAfinderFileForMenu;
#
#
#--------------------------------------------------------------------------------------------------------
# rns
#--------------------------------------------------------------------------------------------------------
# Used for identification of rns
Name = rns
comment = rns_model
order = 5
ToFus = 0
# Identification rns-total:
Item
erpin_arg = "1,29 -add 2 3 -add 4 6 -add 26 27 28 -logzero -5"
cutoff = 3 41 80
model_file = rns-mt.epn
module = 1,2
comment = rns (complete)
comment_for_MFa = complete
EndItem
# Identification rns-5':
Item
erpin_arg = "1,29 -add 2 3 -add 4 6 -logzero -5"
cutoff = 2 38
model_file = rns-mt.epn
module = 1
comment = rns (5' portion)
comment_for_MFa = 5'
EndItem
# Identification rns-3':
Item
erpin_arg = "1,29 -add 27 28 -add 24 26 -logzero -5"
cutoff = 9 42
model_file = rns-mt.epn
module = 2
comment = rns (3' portion)
comment_for_MFa = 3'
EndItem
#--------------------------------------------------------------------------------------------------------
# tRNAs
#--------------------------------------------------------------------------------------------------------
# Used for identification of tRNA
Name = tRNA
comment = tRNA with and without intron
order = 1
ToFus = 1,0,tRNA
Item
erpin_arg = "-1,19 -add 1 17 18 -add 11 12 14 -add 2 3 4 5 7 -logzero -5"
cutoff = 2.9 8 30
model_file = tRNA/tRNA.epn
pos_ac = 13
comment = tRNAs without introns
gap_to_end = 13
evalue_cutoff = 3.4e-03
at_cutoff = 36
EndItem
Item
erpin_arg = "-1,19 -add 1 17 18 -add 11 12 14 -add 2 3 4 5 7 -logzero -5"
cutoff = 9 18 30
model_file = tRNA/yeast.epn
pos_ac = 13
comment = tRNAs without introns
gap_to_end = 13
evalue_cutoff = 3.4e-03
at_cutoff = 36
EndItem
Item
erpin_arg = "-1,26 -add 2 3 5 7 9 -add 1 -add 24 25 -add 11 12 14 -add 16 17 18 20 -logzero -5"
cutoff = 12 18 30 39 60
model_file = tRNA/tRNAint_mt.epn
pos_ac = 13
comment = tRNAs mt with intron
gap_to_end = 13
comment_for_MFa = with intron
to_comment = 1
evalue_cutoff = 3.4e-03
at_cutoff = 36
EndItem
Item
erpin_arg = "-1,26 -add 2 3 5 7 9 -add 1 -add 24 25 -add 11 12 14 -add 16 17 18 20 -logzero -5"
cutoff = 12 18 30 39 60
model_file = tRNA/tRNAint_cp.epn
pos_ac = 13
comment = tRNAs cp with intron
gap_to_end = 13
comment_for_MFa = with intron
to_comment = 1
evalue_cutoff = 3.4e-03
at_cutoff = 36
EndItem
#--------------------------------------------------------------------------------------------------------
# rnpB
#--------------------------------------------------------------------------------------------------------
# Used for identification of rnpB
Name = rnpB
comment = rnpB_model
order = 3
ToFus = 0
# rnpB (RNase P RNA), generale:
Item
erpin_arg = "1,10 -add 2 4 -add 3 5 -add 8 9 -logzero -5"
cutoff = 2.5 12 17
model_file = rnpB-mito.epn
comment = rnpB (mito + plastid)
EndItem
# Derived:
Item
erpin_arg = "1,10 -add 2 4 -add 3 5 -add 8 9 -logzero -5"
cutoff = 2.5 12 15
model_file = rnpB-derived.epn
comment = rnpB, derived (mito + plastid)
EndItem
#--------------------------------------------------------------------------------------------------------
# rrn5
#--------------------------------------------------------------------------------------------------------
# Used for identification of rrn5
Name = rrn5
comment = rrn5_model
order = 4
ToFus = 0
# Partial:
Item
erpin_arg = "1,19 -add 7 8 9 10 -add 4 5 -add 14 15 -add 2 -logzero -5"
cutoff = 15 16 20 24
model_file = 5S-mito.epn
comment = 5S RNA (complete)
comment_for_MFa = complete
EndItem
# Core :
Item
erpin_arg = "1,19 -add 7 8 9 10 -logzero -5"
cutoff = 24
model_file = 5S-mito.epn
comment = 5S RNA (only core region)
comment_for_MFa = only core
EndItem
#--------------------------------------------------------------------------------------------------------
# Introns Group I
#--------------------------------------------------------------------------------------------------------
# Used for identification of group I introns
Name = IntronI
comment = IntronI_model
order = 6
ToFus = 0
Item
erpin_arg = "2,25 -add 2 4 5 6 -add 3 8 9 10 12 17 -add 13 14 15 16 19 21 -logzero -5"
cutoff = 10 21 45
model_file = Introns/B-327.epn
label = IB
comment = intron IB (complete)
EndItem
Item
erpin_arg = "1,22 -add 5 6 7 -add 2 3 8 9 -add 11 12 15 16 17 18 20 21 -logzero -3"
cutoff = 2 6 10
model_file = Introns/IB3-final-1Jan2022.epn
label = IB
comment = intron IB (3)
EndItem
Item
erpin_arg = "1,23 -add 2 4 5 6 -add 3 8 9 10 12 17 -add 13 14 15 16 19 21 22 -logzero -3"
cutoff = 10 15 30
model_file = Introns/IB-final-2Dec2021.epn
label = IB
comment = intron IB (3)
EndItem
Item
erpin_arg = "2,24 -add 4 5 6 -add 3 8 10 -add 9 13 14 15 16 19 21 -logzero -5"
cutoff = 12 26 40
model_file = Introns/B-ins.epn
label = IB
comment = intron IB (extra insertion)
EndItem
Item
erpin_arg = "2,25 -add 2 4 5 6 -add 3 8 9 10 -add 12 17 -logzero -5"
cutoff = 8 12 28
model_file = Introns/B-327.epn
label = IB(5' derived)
comment = intron IB (5', partial)
EndItem
Item
erpin_arg = "2,25 -add 13 14 15 16 17 12 19 21 -logzero -5"
cutoff = 29
model_file = Introns/B-327.epn
label = IB(3' derived)
comment = intron IB (3', partial)
EndItem
Item
erpin_arg = "1,24 -add 2 4 5 6 7 -add 3 8 -add 10 18 15 16 17 -add 11 12 14 20 22 23 -logzero -3"
cutoff = 2 6 8 12
model_file = Introns/IA1-final-2Dec2021.epn
label = IA1
comment = intron IA
EndItem
Item
erpin_arg = "2,21 -add 15 -add 12 13 14 -add 4 -add 8 -add 19 -logzero -5"
cutoff = 7 9 10 11 22
model_file = Introns/Ader.epn
label = I(derived)
comment = intron I (derived, A)
EndItem
Item
erpin_arg = "2,21 -add 15 -add 12 13 14 -add 4 8 19 -logzero -5"
cutoff = 7 11 27
model_file = Introns/Bder1.epn
label = I(derived)
comment = intron I (derived, B1)
EndItem
Item
erpin_arg = "1,22 -add 2 4 5 6 8 -add 9 11 15 -add 3 12 13 14 16 18 20 21 -logzero -3"
cutoff = 3 6 10
model_file = Introns/ID-final-2Dec2021.epn
label = ID
comment = intron ID
EndItem
Item
erpin_arg = "1,25 -add 4 5 6 7 -add 3 2 9 10 11 12 -add 15 16 17 18 19 20 21 24 -logzero -5"
cutoff = 16 36 55
model_file = Introns/B-alt.epn
label = IB
comment = intron IB (extra group)
EndItem
Item
erpin_arg = "1,24 -add 5 6 7 -add 4 8 10 12 13 -add 2 3 15 19 20 -add 16 17 18 22 23 -logzero -3"
cutoff = 4 8 10 20
model_file = Introns/IC1-final-2Dec2021.epn
label = IC1
comment = intron IC1
EndItem
Item
erpin_arg = "1,27 -add 4 5 6 7 9 12 -add 10 11 14 15 2 3 -add 16 17 18 19 21 22 24 25 26 -logzero -3"
cutoff = 6 15 17
model_file = Introns/IC2-final-2Dec2021.epn
label = IC2
comment = intron IC2
EndItem
Item
erpin_arg = "1,23 -add 4 5 6 8 -add 9 10 12 13 -add 3 14 15 16 18 -add 19 21 22 -logzero -3"
cutoff = 8 10 12 14
model_file = Introns/IA3-final-2Dec2021.epn
label = IA3
comment = intron IA3
EndItem
Item
erpin_arg = "2,21 -add 15 -add 12 13 14 -add 4 8 19 -logzero -5"
cutoff = 7 11 27
model_file = Introns/Bder2.epn
label = I(derived)
comment = intron I (derived, B2)
EndItem
#--------------------------------------------------------------------------------------------------------
# Introns Group II
#--------------------------------------------------------------------------------------------------------
# Used for identification of group II introns
Name = IntronII
comment = IntronII_model
order = 7
ToFus = 0
Item
erpin_arg = "1,13 -add 2 3 -add 5 7 9 -logzero -5"
cutoff = 10 20
model_file = Introns/domV-mito-521.epn
label = II
comment = intron II (domainV)
EndItem
Item
erpin_arg = "1,13 -add 2 3 5 7 9 -logzero -5"
cutoff = 25
model_file = Introns/domV-cp-comp.epn
label = II(derived)
comment = intron II, derived
EndItem