Publications - Supplemental material

Please find below supplemental material corresponding to publications of our group. Currently, we list 133 supplements. If you have problems accessing electronic information, please let us know:

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BIOINF 09-009: Temperature-Dependent Structural Variability of RNAs: Spliced Leader RNAs and their Evolutionary History

Manja Marz, Nathalie Vanzo, Peter F. Stadler

For any questions please contact manja@bioinf.uni-leipzig.de

SL RNAs from literatures rewritten by the IUPAC code

IUPAC NT code Base SL-RNAs Dinucleotid shuffling of S. mansoni (300)
R A, G R.txt sma.R.txt
Y C, U Y.txt sma.Y.txt
S C, G S.txt sma.S.txt
W A, U W.txt sma.W.txt
K G, U K.txt sma.K.txt
M A, C M.txt sma.M.txt
B C, G, U B.txt sma.B.txt
D A, G, U D.txt sma.D.txt
H A, C, U H.txt sma.H.txt
V A, C, G V.txt sma.V.txt

SL RNA Alignments

Organism Group ClustalW RNAalifold Locarnate
Euglenida all exon RNAalifold.ps all.stk
Kinetoplastida all exon RNAalifold.ps all.stk
Dinophyceae all exon RNAalifold.ps all.stk
Cnidaria all exon RNAalifold.ps all.stk
Rotifera all exon RNAalifold.ps all.stk
Nematoda all exon SL1.ps SL2.ps all.stk
Platyhelminthes all exon RNAalifold.ps all.stk
Tunicates all exon RNAalifold.ps all.stk
Euglenida/
Kinetoplastida		 all exon all.stk
Euglenida/
Kinetoplastida/
Dinophyceae 		all exon all.stk
Rotifera/
Nematoda		 all exon all.stk SL1.stk SL2.stk
Rotifera/
Nematoda/
Platyhelminthes		 all exon all.stk SL1.stk

SL RNA Secondary structures (done by RNAsubopt -T -C)

Organism Constraints and Structures
E. gracilis TXT
P. curvicauda TXT
C. acus TXT
R. costata TXT
M. pellucidum TXT
E. sulcatum TXT
T. cruzi TXT
T. vivax TXT
T. brucei TXT
L. collosoma TXT
C. fasciculata TXT
L. enriettii TXT
K. brevis TXT
K. micrum TXT
P. piscicida TXT
P. minimum TXT
Hydra TXT
A. ricciae TXT
Philodina sp. TXT
C. elegans TXT
T. spiralis TXT
P. pacificus TXT
H. contortus TXT
S. mansoni TXT
F. hepatica TXT
S. mediterranea TXT
E. multilocularis TXT
C. intestinalis TXT
O. dioica TXT

SL RNA Secondary structures of Stem I

all.known.orgnisms.txt

RNAdistance -Dw -Xm

Structures Input Output
Literature SL_LIT.txt SL_LIT.dist.txt
37 degree SL_37.txt SL_37.dist.txt
Environmental temperature SL_XX.txt SL_XX.dist.txt