Testing Script Readme
How to Test RNA-DM? (http://sourceforge.net/projects/rnadm)
We have submitted our manuscript to Nature Communications for review. In order to help reviewers to test
our software tool, we have generated this document that describes the steps needed to get the results shown
in the figures of our manuscript.
[1] Software Environment Requirement:
[1.1] Hardware:
1. Ubuntu 12.04 or newer system;
2. 8 GB or larger memory;
3. CPU minimum capability is over Intel Core2 2.4Ghz (two cores);
[1.2] Software:
1. Download and Install Vienna RNA package (http://www.tbi.univie.ac.at/RNA/)
2. Download and Install RNAShapes
(http://bibiserv.techfak.uni-bielefeld.de/download/tools/rnashapes.html)
3. Install RNA-DM (download: https://sourceforge.net/projects/rnadm/)
Notice: (1) RNA-DM only works under Linux environment. We have only tested Ubuntu. Presumably, it
should work in other types of Linux like RedHat. (2) In Linux, RNA-DM can be installed in your personal
folder, but we recommend you to install it within /var/local/bin folder.
[2] Input Sequences:
You can use all the sequences described in our supplementary Table-1, which contains both wild-type
sequences and mutant sequences, as the input sequence to test RNA-DM.
mRNA Transcript Name (File Name)
Sequence
SV40 WT (sv40_wildtype.fasta)
AAAUACAAGCUUGUGAUGCUAUUGCUUUAUUUGUAACCAUUAUAAGCUGC
AAUAAACAACUUAACAACAACAAUUGCAUUCAUUUUAUGUUUCAGGUUCA
GGGGGGAGGUGUGGGAGGUUUUUUU
CaMV WT (camv_wildtype.fasta)
CAUAUAAGAAACCCUUAGUAUGUAUUUGUAUUUGUAAAAUACUUCUAUCA
AUAAAAUUUCUAAUUCCUAAAACCAAAAUCCAGUACUAAAAUCCAGAUCU
CCUAAAGUCCCUAUAGAUCUUUGUG
SV40 AAUAAA deletion
AAAUACAAGCUUGUGAUGCUAUUGCUUUAUUUGUAACCAUUAUAAGCUGC
(sv40_noAAUAAA.fasta)
CAACUUAACAACAACAAUUGCAUUCAUUUUAUGUUUCAGGUUCAGGGGGG
AGGUGUGGGAGGUUUUUUU
CaMV AAUAAA deletion
GAGCAUAUAAGAAACCCUUAGUAUGUAUUUGUAUUUGUAAAAUACUUCUA
(camv_noAAUAAA.fasta)
UCAUUUCUAAUUCCUAAAACCAAAAUCCAGUACUAAAAUCCAGAUCUCCU
AAAGUCCCUAUAGAUCUUUGUGUAU
3’end of Arabidopsis Gene AT1G52600
AACAAUUUAAAUACUCGUUUUUGUGGUUAGAUAAUUUUAAAGAGUAGAAU
WT (AT1G52600_3END.fasta)
CUUCUUUUUCCUGUCAAACUAAAUUAUAAACAGUGGAAAGUUAAUUUUUA
GUUGUGGAGACUGGAGAAUGAGUUUACCUAAAAUAUUAAGAUAAGUUAAU
CCUAUGAUCGGUUCCUUCGGGGUCAUCCGAUAAAAUUGAAACGAUACAAA
G
5’end of HIV-1 WT (hiv1_5end.fasta)
GGGUCUCUCUGGUUAGACCAGAUCUGAGCCUGGGAGCUCUCUGGCUAACU
AGGGAACCCACUGCUUAAGCCUCAAUAAAGCUUGCCUUGAGUGCUUCAAG
UAGUGUGUGCCC
Poly(A) region (-50~+50nts) of
CTTCTTTTTCCTGTCAAACTAAATTATAAACAGTGGAAAGTTAATTTTTA
Arabidopsis Gene AT1G52600
GTTGTGGAGACTGGAGAATGAGTTTACCTAAAATATTAAGATAAGTTAAT
(AT1G52600_101NT.fasta)
C
Poly(A) region (-50~+50nts) of HIV-1
CUAGGGAACCCACUGCUUAAGCCUCAAUAAAGCUUGCCUUGAGUGCUUCA
(hiv1_101nt.fasta)
AGUAGUGUGUGCCCGUCUGUUGUGUGACUCUGGUAACUAGAGAUCCCUCA
G
Arabidopsis poly(A) dataset
See the dataset file:
(includes AAUAAA/AUUAAA, 1,990
pnas2010_sense_+_sites_MPSS_support.txt.AATAAA_ATT
sequences)
AAA.seq
(pnas2010_sense_+_sites_MPSS_suppor
t.AATAAA_ATTAAA.fasta)
Arabidopsis poly(A) dataset (no
See the dataset file:
AAUAAA/AUUAAA, 17,899 sequences )
pnas2010_sense_+_sites_MPSS_support.txt.noAATAAA_n
(pnas2010_sense_+_sites_MPSS_suppor
oATTAAA.seq
t.noAATAAA_noATTAAA.fasta)
Human poly(A) dataset (includes
See the dataset file:
AAUAAA/AUUAAA, 405 sequences)
bintian2005_50tag_polyasite.noN_AATAAA_ATTAAA.seq
(bintian2005_50tag_polyasite.noN_AAT
AAA_ATTAAA.fasta)
Human poly(A) dataset (no
See the dataset file:
AAUAAA/AUUAAA, 7,278 sequences )
bintian2005_50tag_polyasite.noN_noAATAAA_noATTAAA.
(bintian2005_50tag_polyasite.noN_noA
seq
ATAAA_noATTAAA.fasta)
Human random dataset (712 sequences)
See the dataset file:
(homo_101nt_Tian_signal.random_seque
homo_101nt_Tian_signal.random_sequence.txt
nce.fasta)
Human poly(A) dataset (includes
homo_101nt_Tian_V5_50est_1sitenum_NUE_AATAAA.txt
AAUAAA, 405 sequences)
(homo_101nt_Tian_V5_50est_1sitenum_
NUE_AATAAA.fasta)
SV40 L WT sequence
AAATACAAGCTTGTGATGCTATTGCTTTATTTGTAACCATTATAAGCTGC
(sv40_L_wildtype.fasta)
AATAAACAAGTTAACAACAACAATTGCATTCATTTTATGTTTCAGGTTCA
GGGGGAGGTGTGGGAGGTTTTTTAA
SV40 L DM3 mutant sequence
AAATACAAGCTTGTGATGCTATTGCTTTATTTGTAACCATTATAAGCTGC
(sv40_L_mutant_DM3.fasta)
AATAAACAAGTTAACAACAACAATTGCATTCATTTTATGTTTCAGGGTAC
CGGGGAGGTGTGGGAGGTTTTTTAA
SV40 L DM2 mutant sequence
AAATACAAGCTTGTGATGCTATTGCTTTATTTGTAACCATTATAAGCTGC
(sv40_L_mutant_DM2.fasta)
AATAAACAAGTTAACAACAACAATTGCATTCACGCGGGAGGTACCGTTCA
GGGGGAGGTGTGGGAGGTTTTTTAA
SV40 L DM4 mutant sequence
AAATACAAGCTTGTGATGCTATTGCTTTATTTGTAACCATTATAAGCTGC
(sv40_L_mutant_DM4.fasta)
AATAAACAAGTTAACAACAACAATTGCATTCATTTTATGTTTCAGGTTCA
ATAGGTACCGTGGGAGGTTTTTTAA
SV40 L aD2 mutant sequence
AAATACAAGCTTGTGATGCTATTGCTTTATTTGTAACCATTATAAGCTGC
(sv40_L_mutant_aD2.fasta)
AATAAACAAGTTAACAACAACAATTGCATTCATTTTAGGTACCCAGGTTC
AGGGGGAGGTGTGGGAGGTTTTTTAA
SV40 L bD2 mutant sequence
AAATACAAGCTTGTGATGCTATTGCTTTATTTGTAACCATTATAAGCTGC
(sv40_L_mutant_bD2.fasta)
AATAAACAAGTTAACAACAACAATTGCATTCATTTTATGTTTCAGGTTCA
GGGGGGTACCTGGGAGGTTTTTTAA
SV40 L abD2 mutant sequence
AAATACAAGCTTGTGATGCTATTGCTTTATTTGTAACCATTATAAGCTGC
(sv40_L_mutant_abD2.fasta)
AATAAACAAGTTAACAACAACAATTGCATTCATTTTAGGTACCCAGGTTC
AGGGGGGTACCTGGGAGGTTTTTTAA
Yeast CYC1 gene WT
UAAACAGGCCCCUUUUCCUUUGUCGAUAUCAUGUAAUUAGUUAUAAUAAA
(cyc1_wildtype.fasta)
CUUACAUUCACGCCCUCCCCCCACAUCCGCUCUAACCGAAAAGGAAGGAG
UUAGACAACCUGAAGUCUAGGUCCC
CaMV Replace UCCGGG mutant
CAUAUAAGAAACCCUUAGUAUGUAUUUGUAUUUGUAAAAUACUUCUAUCU
(camv_UCCGGG.fasta)
CCGGGAUUUCUAAUUCCUAAAACCAAAAUCCAGUACUAAAAUCCAGAUCU
CCUAAAGUCCCUAUAGAUCUUUGUG
CaMV Replace GGGCCC mutant
CAUAUAAGAAACCCUUAGUAUGUAUUUGUAUUUGUAAAAUACUUCUAUCG
(camv_GGGCCC.fasta)
GGCCCAUUUCUAAUUCCUAAAACCAAAAUCCAGUACUAAAAUCCAGAUCU
CCUAAAGUCCCUAUAGAUCUUUGUG
CaMV Replace GUCGAC mutant
CAUAUAAGAAACCCUUAGUAUGUAUUUGUAUUUGUAAAAUACUUCUAUCG
(camv_GUCGAC.fasta)
UCGACAUUUCUAAUUCCUAAAACCAAAAUCCAGUACUAAAAUCCAGAUCU
CCUAAAGUCCCUAUAGAUCUUUGUG
CaMV Replace GUAUUC mutant
CAUAUAAGAAACCCUUAGUAUGUAUUUGUAUUUGUAAAAUACUUCUAUCG
(camv_GUAUUC.fasta)
UAUUCAUUUCUAAUUCCUAAAACCAAAAUCCAGUACUAAAAUCCAGAUCU
CCUAAAGUCCCUAUAGAUCUUUGUG
CaMV Replace UUAUUU mutant
CAUAUAAGAAACCCUUAGUAUGUAUUUGUAUUUGUAAAAUACUUCUAUCU
(camv_UUAUUU.fasta)
UAUUUAUUUCUAAUUCCUAAAACCAAAAUCCAGUACUAAAAUCCAGAUCU
CCUAAAGUCCCUAUAGAUCUUUGUG
rbcs E9 WT (rbcsE9_wildtype.fasta)
UGUAAUUUACUGUGUUUUUUAUUCGGUUUUCGCUAUCGAACUGUGAAAUG
GAAAUGGAUGGAGAAGAGUUAAUGAAUGAUAUGGUCCUUUUGUUCAUUCU
CAAAUUAAUAUUAUUUGUUUUUUCU
rbcs E9 B1 mutant
UGUAAUUUACUGUGUUUUUUAUUCGGUUUUCGCUAUCGAACUGUGAAAUA
(rbcsE9_mutant_B1.fasta)
AAAAUGGAUGGAGAAGAGUUAAUGAAUGAUAUGGUCCUUUUGUUCAUUCU
CAAAUUAAUAUUAUUUGUUUUUUCU
rbcs E9 B2 mutant
UGUAAUUUACUGUGUUUUUUAUUCGGUUUUCGCUAUCGAACUGUGAAUAA
(rbcsE9_mutant_B2.fasta)
AACUCCGAUGGAGAAGAGUUAAUGAAUGAUAUGGUCCUUUUGUUCAUUCU
CAAAUUAAUAUUAUUUGUUUUUUCU
rbcs E9 B3 mutant
UGUAAUUUACUGUGUUUUUUAUUCGGUUUUCGCUAUCGAACUGUGGCGCC
(rbcsE9_mutant_B3.fasta)
GACUCCGAUGGAGAAGAGUUAAUGAAUGAUAUGGUCCUUUUGUUCAUUCU
CAAAUUAAUAUUAUUUGUUUUUUCU
CaMV in Yeast ADH1 Gene WT
CATGTGTTGAGCATATAAGAAACCCTTAGTATGTATTTGTATTTGTAAAA
(ADH1_wildtype_CaMV_insert.fasta)
TACTTCTATCAATAAAATTTCTAATTCCTAAAACCAAAATCCAG
CaMV in Yeast ADH1 Gene mutant
TGTTGAGCATATAAGAAACCCTTAGGCGCTATGTATTTGTATTTGTAAAA
TAGTATGTA -> TAGgcgcTATGTA
TACTTCTATCAATAAAATTTCTAATTCCTAAAACCAAAATCCAG
(ADH1_mutant_TAGTATGTA_to_TAG
gcgcTATGTA.fasta)
CaMV in Yeast ADH1 Gene mutant
CATGTGTTGAGCATATAAGAAACCCTTTTTTTATATTTGTATTTGTAAAA
TAGTATGTA -> TTTTTTATA
TACTTCTATCAATAAAATTTCTAATTCCTAAAACCAAAATCCAG
(ADH1_mutant_TAGTATGTA_to_TTT
TTTATA.fasta)
CaMV in Yeast ADH1 Gene mutant
TGTTGAGCATATAAGAAACCCTTAGATATTATGTATTTGTATTTGTAAAA
TAGTATGTA -> TAGatatTATGTA
TACTTCTATCAATAAAATTTCTAATTCCTAAAACCAAAATCCAG
(ADH1_mutant_TAGTATGTA_to_TAGa
tatTATGTA.fasta)
Yeast ADH1 Gene mutant del -29
CGCTCATGTGTTGAGCATATAAGAAACCCTTAGTATGTATTTGTATTTGT
(ADH1_mutant_del-29.fasta)
AAACTAAAACCAAAATCCAG
Yeast ADH1 Gene mutant del -8
AGAAACCCTTAGTATGTATTTGTATTTGTAAAATACTTCTATCAATAAAA
(ADH1_mutant_del-8.fasta)
TTTCTAAAACCAAAATCCAG
Yeast ADH1 Gene WT
CTTAGTATGTATTTGTATTTGTAAAATACTTCTATCAATAAAATTTCTAA
(ADH1_wildtype.fasta)
TTCCTAAAACCAAAATCCAG
Yeast ADH1 Gene mutant del +10
AAACCCTTAGTATGTATTTGTATTTGTAAAATACTTCTATCAATAAAATT
(ADH1_mutant_del+10.fasta)
TCTAATTCCTAAAACCAAAA
FMV WT (fmv_wildtype.fasta)
AUCUUGUAAUGGAUCCAAGUGUCUGUAAUUUUUGGAAAAAUUGAUCUAUA
AAAUAUUCAAUCUUUCUUUAAGCUUAUUCAAAGAACAAACAUACUAUCUA
UCAUCCAAAUCCACAGAGUGACAGA
FMV WT (-150 ~+150nts )
AGGCTAAGACCCTAAAGAGTTTCGAAAGAGAAATGTAGTATAGTAAGAGT
(fmv_wildtype_301nt.fasta)
CCTCCCAGTCCGGGAGATTGTAATAAAGAGATCTTGTAATGGATCCAAGT
GTCTGTAATTTTTGGAAAAATTGATCTATAAAATATTCAATCTTTCTTTA
AGCTTATTCAAAGAACAAACATACTATCTATCATCCAAATCCACAGAGTG
ACAGAGAGAAAATGGTCTGTGTTGTGTGGATCTGAAGTACCGCCGAGGCA
GGAGGCCGTTAGGGAAAAAGGGACTGTTTTGACCGTCAAAGTATCAGGCT
RTBV WT (125nts )
TGTTTGTACTTATGATTGTATTTCTCAAAACCTATCCGCTGCATGAATAA
(rtbv_wildtype_125nt.fasta)
AGCTCTTATATTTATCCTACACCCTTGTGATAAAACATGAAGTCATACTC
GTTCTAAGATTAAGTGTTCTAAAAA
RTBV WT (-150 ~+150nts )
TCTTCAAGAAGCAAAGGCGATCAATGGCTCAGGTCAGTGAGTAGTCGTCT
(rtbv_wildtype_301nt.fasta)
TTAAGGTTCCTCTAGGAACCTCTGTGTAATATGTTTGTACTTATGATTGT
ATTTCTCAAAACCTATCCGCTGCATGAATAAAGCTCTTATATTTATCCTA
CACCCTTGTGATAAAACATGAAGTCATACTCGTTCTAAGATTAAGTGTTC
TAAAAATACTTCGAAGCATTGAAAAGGGGGCTAAAGGGGGAAAAAGTACC
GTCAGGCCGTGTTATGGCAAGGGAAGAAGTACCATGAATACCCTATAGAT
G
T-DNA-encoded octopine synthase
CGGUUUCGGUUCAUUCUAAUGAAUAUAUCACCCGUUACUAUCGUAUUUUU
(OCS) WT (125nts)
AUGAAUAAUAUUCUCCGUUCAAUUUACUGAUUGUACCCUACUACUUAUAU
(ocs_wildtype_125nt.fasta)
GUACAAUAUUAAAAUGAAAACAAUA
T-DNA-encoded octopine synthase
TATGATCGCATGATATTTGCTTTCAATTCTGTTGTGCACGTTGTAAAAAA
(OCS) WT (-150 ~+150nts)
CCTGAGCATGTGTAGCTCAGATCCTTACCGCCGGTTTCGGTTCATTCTAA
(ocs_wildtype_301nt.fasta)
TGAATATATCACCCGTTACTATCGTATTTTTATGAATAATATTCTCCGTT
CAATTTACTGATTGTACCCTACTACTTATATGTACAATATTAAAATGAAA
ACAATATATTGTGCTGAATAGGTTTATAGCGACATCTATGATAGAGCGCC
ACAATAACA
Yeast ADH2 gene WT (125nts)
CCUAUAUUAGUAUAUAGCAUCUUUAGAUGACAGUGUUCGAAGUUUCACGA
(ADH2_125nt_wildtype.fasta)
AUAAAAGAUAAUAUUCUACUUUUUGCUCCCACCGCGUUUGCUAGCACGAG
UGAACACCAUCCCUCGCCUGUGAGU
CaMV WT (-150 ~+150nts)
CTATCTCTCTCTATAATAATGTGTGAGTAGTTCCCAGATAAGGGAATTAG
(camv_wildtype_301nt.fasta)
GGTTCTTATAGGGTTTCGCTCATGTGTTGAGCATATAAGAAACCCTTAGT
ATGTATTTGTATTTGTAAAATACTTCTATCAATAAAATTTCTAATTCCTA
AAACCAAAATCCAGTACTAAAATCCAGATCTCCTAAAGTCCCTATAGATC
TTTGTGGTGAATATAAACCAGACACGAGACGACTAAACCTGGAGCCCAGA
CGC
Yeast CYC1 gene WT (-150 ~+150nts)
TACCAAGATGGCCTTTGGTGGGTTGAAGAAGGAAAAAGACAGAAACGACT
(cyc1_wildtype_301nt.fasta)
TAATTACCTACTTGAAAAAAGCCTGTGAGTAAACAGGCCCCTTTTCCTTT
GTCGATATCATGTAATTAGTTATAATAAACTTACATTCACGCCCTCCCCC
CACATCCGCTCTAACCGAAAAGGAAGGAGTTAGACAACCTGAAGTCTAGG
TCCCTATTTATTTTTTTATAGTTATGTTAGTATTAAGAACGTTATTTATA
TTTCAAATTTTTCTTTTTTTTCTGTACAGACGCGTGTACGCATGTAACAT
rbcs E9 WT (-150 ~+150nts)
UUGCGCACACACCAGAAUCCUACUGAGUUCGAGUAUUAUGGCAUUGGGAA
(rbcsE9_wildtype_301nt.fasta)
AACUGUUUUUCUUGUACCAUUUGUUGUGCUUGUAAUUUACUGUGUUUUUU
AUUCGGUUUUCGCUAUCGAACUGUGAAAUGGAAAUGGAUGGAGAAGAGUU
AAUGAAUGAUAUGGUCCUUUUGUUCAUUCUCAAAUUAAUAUUAUUUGUUU
UUUCUCUUAUUUGUUGUGUGUUGAAUUUGAAAUUAUAAGAGAUAUGCAAA
CAUUUUGUUUUGAGUAAAAAUGUGUCAAAUCGUGGCCUCUAAUGACCGAA
SV40 WT (-150 ~+150nts)
CTGCAATAAACAAGTTAACAACAACAATTGCATTCATTTTATGTTTCAGG
(sv40_wildtype_301nt.fasta)
TTCAGGGGGAGGTGTGGGAGGTTTTTTAAAGCAAATACAAGCTTGTGATG
CTATTGCTTTATTTGTAACCATTATAAGCTGCAATAAACAACTTAACAAC
AACAATTGCATTCATTTTATGTTTCAGGTTCAGGGGGGAGGTGTGGGAGG
TTTTTTAAATTATTTGTGAAATTTGTGATGCTATTGCTTTATTTGTAACC
ATTATAAGCTGC
[3] The commands and parameters to get the data shown in each figure of our manuscript
[3.1] Fig.1
SV40 secondary structure was predicted by RNAShapes:
./RNAshapes -q -f sv40_wildtype.fasta >SV40.dbf
Notice:
sv40_wildtype.fasta includes the sv40 wild-type sequence in .fasta format.
SV40.dbf includes the output result in dot-bracket format.
[3.2] Fig.2
Arabidopsis Gene AT1G52600 and HIV-1 3’end secondary structures were predicted by RNAFold.
./RNAFold -p --MEA -d1 --noLP -T 22 AT1G52600_3END.fasta >AT1G52600.dbf
./RNAFold -p --MEA -d1 --noLP -T 37 hiv1_5end.fasta >HIV1.dbf
Notice:
AT1G52600_3END.fasta includes wild-type sequence in 3’end.
AT1G52600.dbf includes the secondary structure that based on dot-bracket format.
hiv1_5end.fasta includes wild-type sequence in 5’end.
HIV1.dbf includes the secondary structure that based on dot-bracket format.
RNA dynamic landscape curves of AT1G52600 and HIV-1 were produced by RNA-DM.
./rnadm --input_file AT1G52600_101NT.fasta --seqlength 101 --scanwindow 30 --scanstep 1 --T 22
./rnadm --input_file hiv1_101nt.fasta --seqlength 101 --scanwindow 30 --scanstep 1 --T 37
Notice:
RNA-DM will output a series free-energy values for continuous scan windows. User may need use some the
third part tools to convert these values to curve, such as Excel, SPSS and R etc.
[3.3] Fig.3
Arabidopsis and Human AAUAAA/AUUAAA dataset dynamic landscape
./rnadm --input_file pnas2010_sense_+_sites_MPSS_support.AATAAA_ATTAAA.fasta --seqlength 101
--scanwindow 30 --scanstep 1 --T 25
./rnadm --input_file pnas2010_sense_+_sites_MPSS_support.noAATAAA_noATTAAA.fasta --seqlength
101 --scanwindow 30 --scanstep 1 --T 25
./rnadm --input_file bintian2005_50tag_polyasite.noN_AATAAA_ATTAAA.fasta --seqlength 101
--scanwindow 30 --scanstep 1 --T 37
./rnadm --input_file bintian2005_50tag_polyasite.noN_noAATAAA_noATTAAA.fasta --seqlength 101
--scanwindow 30 --scanstep 1 --T 37
[3.4] Fig.4
SV40 L secondary structure was predicted by RNAShapes.
./RNAshapes -q -f sv40_L_wildtype.fasta >SV40_L.dbf
The integrity of U/GU-rich hairpin was processed by our in-house algorithm.
The algorithm is that
Notice:
Probability is the potential structure probability.
Entirety is the percentage of pairing relative to wild-type
in U/GU-rich hairpin, was shown as rectangle in figure. We collected all situations in potential structure
group. The minimum of potential structure probability must larger than 10%.
[3.5] Fig.5
SV40 L secondary structure was predicted by RNAShapes.
./RNAshapes -q -f sv40_L_wildtype.fasta >SV40_L.dbf
Notice:
We only consider the cases that structural probability over 10%.
[3.6] Fig.6
CaMV secondary structure was predicted by RNAShapes.
./RNAshapes -q -f Camv_wildtype.fasta >CaMV.dbf
Notice:
We only consider the cases that structural probability over 10%.
[3.7] Fig.7
Yeast CYC1 secondary structure was predicted by RNAShapes.
./RNAshapes -q -f cyc1_wildtype.fasta >CYC1.dbf
Notice:
We only consider the cases that structural probability over 10%.
[3.8] Fig.8
(1) CaMV
CaMV mutant structures was predicted by RNAShapes.
./RNAshapes -q -f camv_UCCGGG.fasta >camv_UCCGGG.dbf
./RNAshapes -q -f camv_GGGCCC.fasta >camv_GGGCCC.dbf
./RNAshapes -q -f camv_GUCGAC.fasta >camv_GUCGAC.dbf
./RNAshapes -q -f camv_GUAUUC.fasta >camv_GUAUUC.dbf
./RNAshapes -q -f camv_UUAUUU.fasta >camv_UUAUUU.dbf
./RNAshapes -q -f camv_noAAUAAA.fasta >camv_noAAUAAA.dbf
Notice:
camv_mutant_seq.fasta includes 6 mutant sequences and wild-type sequence.
camv_mutant.dbf includes all potential structures and free-energy values for mutant and wild-type
sequences.
We only consider the cases that structural probability over 10%.
(2) rbcs E9
rbcs E9 mutant structures was predicted by RNAShapes.
./RNAshapes -q -f rbcsE9_mutant_B1.fasta >rbcse9_mutant_B1.dbf
./RNAshapes -q -f rbcsE9_mutant_B2.fasta >rbcse9_mutant_B2.dbf
./RNAshapes -q -f rbcsE9_mutant_B3.fasta >rbcse9_mutant_B3.dbf
Notice:
rbcse9_mutant_seq.fasta includes 3 mutant sequences and wild-type sequence.
rbcse9_mutant.dbf includes all potential structures and free-energy values for mutant and wild-type
sequences.
We only consider the cases that structural probability over 10%.
(3) CaMV in Yeast C
Yeast mutant structures was predicted by RNAShapes.
./RNAshapes -q -f yeast_c_mutant_seq.fasta >yeast_c_mutant.dbf
./RNAshapes -q -f ADH1_mutant_TAGTATGTA_to_TAGgcgcTATGTA.fasta
>yeast_c_TAGTATGTA_to_TAGgcgcTATGTA.dbf
./RNAshapes -q -f ADH1_mutant_TAGTATGTA_to_TTTTTTATA.fasta
>yeast_c_TAGTATGTA_to_TTTTTTATA.dbf
./RNAshapes -q -f ADH1_mutant_TAGTATGTA_to_TAGatatTATGTA.fasta
>yeast_c_TAGTATGTA_to_TAGatatTATGTA.dbf
Notice:
yeast_c_mutant_seq.fasta includes 3 mutant sequences and wild-type sequence.
yeast_c_mutant.dbf includes all potential structures and free-energy values for mutant and wild-type
sequences.
We only consider the cases that structural probability over 10%.
(4) Yeast D
Yeast D mutant structures was predicted by RNAShapes.
./RNAshapes -q -f yeast_d_mutant_seq.fasta >yeast_d_mutant.dbf
./RNAshapes -q -f ADH1_mutant_del-29.fasta >yeast_d_del-29.dbf
./RNAshapes -q -f ADH1_mutant_del-8.fasta >yeast_d_del-8.dbf
./RNAshapes -q -f ADH1_mutant_del+10.fasta >yeast_d_del+10.dbf
Notice:
yeast_d_mutant_seq.fasta includes 3 mutant sequences and wild-type sequence.
yeast_d_mutant.dbf includes all potential structures and free-energy values for mutant and wild-type
sequences.
We only consider the cases that structural probability over 10%.