TY - JOUR AU - Shapiro, B. AU - Zhang, K. PY - 1990 DA - 1990// TI - Comparing multiple RNA secondary structures using tree comparisons JO - Comput Appl Biosci VL - 6 ID - Shapiro1990 ER - TY - JOUR AU - Hofacker, I. L. AU - Bernhart, S. H. F. AU - Stadler, P. F. PY - 2004 DA - 2004// TI - Alignment of RNA base pairing probability matrices JO - Bioinformatics VL - 20 UR - https://doi.org/10.1093/bioinformatics/bth229 DO - 10.1093/bioinformatics/bth229 ID - Hofacker2004 ER - TY - JOUR AU - McCaskill, J. S. PY - 1990 DA - 1990// TI - The equilibrium partition function and base pair binding probabilities for RNA secondary structure JO - Biopolymers VL - 29 UR - https://doi.org/10.1002/bip.360290621 DO - 10.1002/bip.360290621 ID - McCaskill1990 ER - TY - JOUR AU - Le, S. Y. AU - Nussinov, R. AU - Maizel, J. V. PY - 1989 DA - 1989// TI - Tree graphs of RNA secondary structures and their comparisons JO - Comput Biomed Res VL - 22 UR - https://doi.org/10.1016/0010-4809(89)90039-6 DO - 10.1016/0010-4809(89)90039-6 ID - Le1989 ER - TY - JOUR AU - Shapiro, B. PY - 1988 DA - 1988// TI - An algorithm for comparing multiple RNA secondary structures JO - Comput Appl Biosci VL - 4 ID - Shapiro1988 ER - TY - JOUR AU - Sankoff, D. PY - 1985 DA - 1985// TI - Simultaneous solution of the RNA folding, alignment, and protosequence problems JO - SIAM J Appl Math VL - 45 UR - https://doi.org/10.1137/0145048 DO - 10.1137/0145048 ID - Sankoff1985 ER - TY - JOUR AU - Le, S. Y. AU - Owens, J. AU - Nussinov, R. AU - Chen, J. H. AU - Shapiro, B. AU - Maizel, J. V. PY - 1989 DA - 1989// TI - RNA secondary structures: comparisons and determination of frequently recurring substructures by consensus JO - Comput Appl Biosci VL - 5 ID - Le1989 ER - TY - JOUR AU - Jiang, T. AU - Lin, G. H. AU - Ma, B. AU - Zhang, K. PY - 2002 DA - 2002// TI - A general edit distance between RNA structures JO - Journal of Computational Biology VL - 9 UR - https://doi.org/10.1089/10665270252935511 DO - 10.1089/10665270252935511 ID - Jiang2002 ER - TY - JOUR AU - Liao, B. AU - Wang, T. M. PY - 2004 DA - 2004// TI - A 3D graphical representation of RNA secondary structure JO - J Biomol Struc Dynamics VL - 21 UR - https://doi.org/10.1080/07391102.2004.10506972 DO - 10.1080/07391102.2004.10506972 ID - Liao2004 ER - TY - JOUR AU - Randic, M. AU - Basak, S. C. PY - 2001 DA - 2001// TI - Characterization of DNA primary sequences based on the average distances between bases JO - J Chem Inf Comput Sci VL - 41 UR - https://doi.org/10.1021/ci0000981 DO - 10.1021/ci0000981 ID - Randic2001 ER - TY - JOUR AU - Zupan, J. AU - Randic, M. PY - 2005 DA - 2005// TI - Algorithm for coding DNA sequences into "spectrum-like" and "zigzag" representations JO - J Chem Inf Comput Sci VL - 45 UR - https://doi.org/10.1021/ci040104j DO - 10.1021/ci040104j ID - Zupan2005 ER - TY - JOUR AU - Guo, X. F. AU - Nandy, A. PY - 2003 DA - 2003// TI - Numerical characterization of DNA sequences in a 2-D graphical representation scheme of low degeneracy JO - Chemical Physics Letters VL - 369 UR - https://doi.org/10.1016/S0009-2614(02)02029-8 DO - 10.1016/S0009-2614(02)02029-8 ID - Guo2003 ER - TY - JOUR AU - Randic, M. AU - Vracko, M. AU - Lers, N. AU - Plavsic, D. PY - 2003 DA - 2003// TI - Analysis of similarity/dissimilarity of DNA sequences based on novel 2-D graphical representation JO - Chemical Physics Letters VL - 371 UR - https://doi.org/10.1016/S0009-2614(03)00244-6 DO - 10.1016/S0009-2614(03)00244-6 ID - Randic2003 ER - TY - CHAP AU - Hochsmann, M. AU - Toller, T. AU - Giegerich, R. AU - Kurtz, S. PY - 2003 DA - 2003// TI - Local similarity in RNA secondary structures BT - Proceedings of the IEEE Bioinformatics Conference 2003 (CSB 2003) ID - Hochsmann2003 ER - TY - JOUR AU - Lempel, A. AU - Ziv, J. PY - 1976 DA - 1976// TI - On the complexity of finite sequences JO - IEEE T Inform Theory VL - 22 UR - https://doi.org/10.1109/TIT.1976.1055501 DO - 10.1109/TIT.1976.1055501 ID - Lempel1976 ER - TY - JOUR AU - Brown, J. PY - 1998 DA - 1998// TI - The ribonuclease P database JO - Nucleic Acids Res VL - 26 UR - https://doi.org/10.1093/nar/26.1.351 DO - 10.1093/nar/26.1.351 ID - Brown1998 ER - TY - JOUR AU - Schmitt, M. AU - Bennett, J. AU - Dairaghi, D. PY - 1993 DA - 1993// TI - Secondary structure of RNase MRP RNA as predicted by phylogenetic comparison JO - FASEB J VL - 7 ID - Schmitt1993 ER - TY - JOUR AU - Szymanski, M. AU - Miroslawa, Z. AU - Barciszewska, V. A. AU - Barciszewski, E. J. PY - 2002 DA - 2002// TI - 5S ribosomal RNA database JO - Nucleic Acids Res VL - 30 UR - https://doi.org/10.1093/nar/30.1.176 DO - 10.1093/nar/30.1.176 ID - Szymanski2002 ER - TY - JOUR AU - Felsenstein, J. PY - 1989 DA - 1989// TI - PHYLIP-Phylogeny inference package (version 3.2) JO - Cladistics VL - 5 ID - Felsenstein1989 ER - TY - JOUR AU - Page, R. D. M. PY - 1996 DA - 1996// TI - TREEVIEW: An application to display phylogenetic trees on personal computers JO - Computer Applications in the Biosciences VL - 12 ID - Page1996 ER - TY - JOUR AU - Hiro, H. AU - Osawa, S. PY - 1979 DA - 1979// TI - Evolutionary change in 5S rRNA secondary structure and a phylogenetic tree of 54 5S rRNA species JO - Proc Natl Acad Sci USA VL - 76 UR - https://doi.org/10.1073/pnas.76.1.381 DO - 10.1073/pnas.76.1.381 ID - Hiro1979 ER - TY - JOUR AU - Hiro, H. AU - Osawa, S. PY - 1986 DA - 1986// TI - Evolutionary change in 5S rRNA secondary structure and a phylogenetic tree of 352 5S rRNA species JO - Proc Natl Acad Sci USA VL - 19 ID - Hiro1986 ER - TY - JOUR AU - Morrissey, J. P. AU - Tollervey, D. PY - 1995 DA - 1995// TI - Birth of the snoRNPs: the evolution of RNase MRP and the eukaryotic pre-rRNA-processing system JO - TIBS VL - 20 ID - Morrissey1995 ER - TY - JOUR AU - Reddy, R. AU - Shimba, S. PY - 1996 DA - 1996// TI - Structural and functional similarities between MRP and RNase P JO - Mol Biol Rep VL - 22 UR - https://doi.org/10.1007/BF00988710 DO - 10.1007/BF00988710 ID - Reddy1996 ER - TY - JOUR AU - Chamberlain, J. AU - Pagan-Ramos, E. AU - Kindelberger, D. AU - Engelke, D. PY - 1996 DA - 1996// TI - An RNase P RNA subunit mutation affects ribosomal RNA processing JO - Nucleic Acids Res VL - 24 UR - https://doi.org/10.1093/nar/24.16.3158 DO - 10.1093/nar/24.16.3158 ID - Chamberlain1996 ER - TY - JOUR AU - Collins, L. J. AU - Moulton, V. AU - Penny, D. PY - 2000 DA - 2000// TI - Use of RNA secondary structure for studying the evolution of RNase P and RNase MRP JO - J Mol Evol VL - 51 ID - Collins2000 ER - TY - JOUR AU - Höchsmann, M. AU - Voss, B. AU - Giegerich, R. PY - 2004 DA - 2004// TI - Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach JO - IEEE ICBB VL - 1 ID - Höchsmann2004 ER - TY - JOUR AU - Otu, H. H. AU - Sayood, K. PY - 2003 DA - 2003// TI - A new sequence distance measure for phylogenetic tree construction JO - Bioinformatics VL - 19 UR - https://doi.org/10.1093/bioinformatics/btg295 DO - 10.1093/bioinformatics/btg295 ID - Otu2003 ER -