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==References== {{reflist|30em|refs=<ref name="Chomsky_1956">{{cite journal |author=Chomsky, Noam|title= Three models for the description of language. |journal=IRE Transactions on Information Theory|volume=2|issue= 3 |pages=113–124|year=1956|doi= 10.1109/TIT.1956.1056813|s2cid= 19519474 }}</ref> <ref name="Chomsky_1959">{{cite journal |author=Chomsky, Noam |title=On certain formal properties of grammars |journal=Information and Control |date=June 1959 |volume=2 |issue=2 |pages=137–167 |doi=10.1016/S0019-9958(59)90362-6|doi-access=free }}</ref> <ref name="Chomsky_1957">{{cite book |editor=Noam Chomsky|title=Syntactic Structures.|publisher= Mouton & Co. Publishers, Den Haag, Netherlands|year= 1957}}</ref> <ref name="Eddy 1994">{{cite journal |author1=Eddy S. R. |author2=Durbin R. |name-list-style=amp |title=RNA sequence analysis using covariance models|journal=Nucleic Acids Research|volume=22|pages=2079–2088|year=1994|doi=10.1093/nar/22.11.2079|pmid=8029015|pmc=308124|issue=11}}</ref> <ref name="Sakakibara 1994">{{cite journal |author=Sakakibara Y. |author2=Brown M. |author3=Hughey R. |author4=Mian I. S. |display-authors=etal |title=Stochastic context-free grammars for tRNA modelling |journal=Nucleic Acids Research |volume=22 |issue= 23 |pages=5112–5120 |year=1994 |doi=10.1093/nar/22.23.5112|pmid=7800507 |pmc=523785 }}</ref> <ref name="Grat 1995">{{cite journal|author=Grat, L.|title=Automatic RNA secondary structure determination with stochastic context-free grammars|journal=In Rawlings, C., Clark, D., Altman, R., Hunter, L., Lengauer, T and Wodak, S. Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology, AAAI Press|pages=136–144|url=http://www.aaai.org/Papers/ISMB/1995/ISMB95-017.pdf|year=1995|access-date=2017-08-03|archive-date=2015-12-04|archive-url=https://web.archive.org/web/20151204013359/http://www.aaai.org/Papers/ISMB/1995/ISMB95-017.pdf|url-status=dead}}</ref> <ref name="Lefebvre 1995">{{cite book |author=Lefebvre, F |contribution=An optimized parsing algorithm well suited to RNA folding |editor=Rawlings, C. |editor2=Clark, D. |editor3=Altman, R. |editor4=Hunter, L. |editor5=Lengauer, T. |editor6=Wodak, S. |title=Proceedings of the Third International Conference on Intelligent Systems for Molecular Biology |publisher=AAAI Press |pages=222–230 |date=1995|url=https://www.aaai.org/Papers/ISMB/1995/ISMB95-027.pdf}}</ref> <ref name="Lefebvre 1996">{{cite book |last=Lefebvre |first=F. |contribution=A grammar-based unification of several alignment and folding algorithms |editor=States, D. J. |editor2=Agarwal, P. |editor3=Gaasterlan, T. |editor4=Hunter, L. |editor5=Smith R. F. |title=Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology |publisher=AAAI Press |pages=143–153 |date=1996|url=https://www.aaai.org/Papers/ISMB/1996/ISMB96-016.pdf}}</ref> <ref name="Durbin 1998">{{cite book |author1=R. Durbin |author2=S. Eddy |author3=A. Krogh |author4=G. Mitchinson |title=Biological sequence analysis: probabilistic models of proteins and nucleic acids |url=https://books.google.com/books?id=R5P2GlJvigQC |publisher=Cambridge University Press |year=1998 |isbn=978-0-521-62971-3}}</ref> <ref name="Dowell 2004">{{cite journal |author=Dowell R. |author2=Eddy S.|name-list-style=amp |title=Evaluation of several lightweight stochastic context-free grammars for RNA secondary structure prediction|journal=BMC Bioinformatics |volume=5|issue=71|pages=71 |doi=10.1186/1471-2105-5-71|pmid=15180907 |pmc=442121 |year=2004 |doi-access=free }}</ref> <ref name="McCaskill 1990">{{cite journal |author=McCaskill J. S.|title= The Equilibrium Partition Function and Base Pair Binding Probabilities for RNA Secondary Structure |journal=Biopolymers|volume=29|pages=1105–19|year=1990|doi=10.1002/bip.360290621|pmid=1695107|issue=6–7|hdl= 11858/00-001M-0000-0013-0DE3-9 |s2cid= 12629688 |hdl-access=free}}</ref> <ref name="Juan 1999">{{cite journal |author=Juan V. |author2=Wilson C. |title= RNA Secondary Structure Prediction Based on Free Energy and Phylogenetic Analysis|journal=J. Mol. Biol.|volume= 289|issue= 4|pages=935–947|year=1999|doi=10.1006/jmbi.1999.2801|pmid= 10369773}}</ref> <ref name="Zuker 2000">{{cite journal |author=Zuker M|title= Calculating Nucleic Acid Secondary Structure|journal=Curr. Opin. Struct. Biol.|volume=10|issue= 3|pages=303–310|year=2000|doi=10.1016/S0959-440X(00)00088-9|pmid= 10851192}}</ref> <ref name="Mathews 1999">{{cite journal |author1=Mathews D. H. |author2=Sabina J. |author3=Zuker M. |author4=Turner D. H. |title= Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure|journal=J. Mol. Biol.|volume=288|pages=911–940|year=1999|doi=10.1006/jmbi.1999.2700|pmid=10329189|issue=5|s2cid=19989405 |doi-access=free}}</ref> <ref name="Knudsen 2003">{{cite journal |author1=B. Knudsen |author2=J. Hein. |name-list-style=amp |title= Pfold: RNA secondary structure prediction using stochastic context-free grammars |journal=Nucleic Acids Research |volume=31|issue=13|pages=3423–3428|year=2003|doi=10.1093/nar/gkg614 |pmid=12824339 |pmc=169020}}</ref> <ref name="Knudsen 1999">{{cite journal |author=Knudsen B. |author2=Hein J. |title= RNA Secondary Structure Prediction Using Stochastic Context-Free Grammars and Evolutionary History |journal=Bioinformatics|volume=15|pages=446–454|year=1999|doi=10.1093/bioinformatics/15.6.446|pmid=10383470|issue=6|doi-access=free}}</ref> <ref name="Rivas 2001">{{cite journal |author=Rivas E. |author2=Eddy S. R. |title= Noncoding RNA Gene Detection Using Comparative Sequence Analysis |journal=BMC Bioinformatics|volume=2|year=2001|doi=10.1186/1471-2105-2-8|pmid=11801179|pmc=64605|issue=1|pages=8 |doi-access=free }}</ref> <ref name="Holmes 2002">{{cite book|author=Holmes I.|author2=Rubin G. M.|title=Pairwise RNA Structure Comparison with Stochastic Context-Free Grammars|journal=In. Pac. Symp. Biocomput.|pages=[https://archive.org/details/pacificsymposium00paci/page/163 163–174]|year=2002|doi=10.1142/9789812799623_0016|pmid=11928472|isbn=978-981-02-4777-5|url-access=registration|url=https://archive.org/details/pacificsymposium00paci/page/163}}</ref> <ref name="Gardner 2010">{{cite journal |author1=P. P. Gardner |author2=J. Daub |author3=J. Tate |author4=B. L. Moore |author5=I. H. Osuch |author6=S. Griffiths-Jones |author7=R. D. Finn |author8=E. P. Nawrocki |author9=D. L. Kolbe |author10=S. R. Eddy |author11=A. Bateman. |title=Rfam: Wikipedia, clans and the "decimal" release |journal=Nucleic Acids Research|year=2011|volume=39|doi=10.1093/nar/gkq1129|pmid=21062808|pmc=3013711|issue=Suppl 1|pages=D141–D145}}</ref> <ref name="Yao 2006">{{cite journal |author=Yao Z. |author2=Weinberg Z. |author3=Ruzzo W. L. |title=CMfinder-a covariance model based RNA motif finding algorithm |journal=Bioinformatics|volume=22 |pages=445–452|year=2006|doi=10.1093/bioinformatics/btk008|pmid=16357030|issue=4|doi-access=free}}</ref> <ref name="Rabani 2008">{{cite journal |author=Rabani M. |author2=Kertesz M. |author3=Segal E. |title= Computational prediction of RNA structural motifs involved in post-transcriptional regulatory processes |journal= Proc. Natl. Acad. Sci. USA|volume=105|issue= 39 |pages=14885–14890|year=2008|doi=10.1073/pnas.0803169105 |pmid= 18815376 |pmc=2567462|bibcode=2008PNAS..10514885R |doi-access=free }}</ref> <ref name="Goodarzi 2012">{{cite journal |author=Goodarzi H. |author2=Najafabadi H. S. |author3=Oikonomou P. |author4=Greco T. M. |author5=Fish L. |author6=Salavati R. |author7=Cristea I. M. |author8=Tavazoie S. |title= Systematic discovery of structural elements governing stability of mammalian messenger RNAs |journal=Nature |volume=485 |issue= 7397 |pages=264–268 |year=2012 |doi=10.1038/nature11013 |pmid=22495308 |pmc=3350620|bibcode=2012Natur.485..264G }}</ref> <ref name="Sipser 1996">{{cite book |author=Sipser M.|title= Introduction to Theory of Computation|publisher=Brooks Cole Pub Co.|year=1996}}</ref> <ref name="Harrison 1978">{{cite book |author=Michael A. Harrison |title= Introduction to Formal Language Theory |publisher=Addison-Wesley|year=1978|author-link= Michael A. Harrison }}</ref> <ref name="Hopcroft 1979">{{cite book |author1=Hopcroft J. E. |author2=Ullman J. D. |title= Introduction to Automata Theory, Languages, and Computation |publisher=Addison-Wesley|year=1979}}</ref> <ref name="Giegerich 2000">{{cite book |author=Giegerich R.|title=Combinatorial Pattern Matching |chapter=Explaining and Controlling Ambiguity in Dynamic Programming |publisher= In Proceedings of the 11th Annual Symposium on Combinatorial Pattern Matching 1848 Edited by: Giancarlo R., Sankoff D. Montréal, Canada: Springer-Verlag, Berlin|series=Lecture Notes in Computer Science|pages=46–59|year=2000|volume=1848|doi=10.1007/3-540-45123-4_6|isbn=978-3-540-67633-1|s2cid=17088251}}</ref> <ref name="Lari and Young 1990">{{cite journal |author1=Lari K. |author2=Young S. J. |title= The estimation of stochastic context-free grammars using the inside-outside algorithm |journal=Computer Speech and Language|volume=4|pages=35–56|year=1990|doi=10.1016/0885-2308(90)90022-X}}</ref> <ref name="Lari and Young 1991">{{cite journal |author1=Lari K. |author2=Young S. J. |title= Applications of stochastic context-free grammars using the inside-outside algorithm|journal=Computer Speech and Language|volume=5|issue=3 |pages=237–257|year=1991|doi=10.1016/0885-2308(91)90009-F}}</ref> <ref name="Nawrocki 2013">{{cite journal| author=Nawrocki E. P., Eddy S. R.|title=Infernal 1.1:100-fold faster RNA homology searches|journal=Bioinformatics|volume=29|pages=2933–2935|year=2013|doi=10.1093/bioinformatics/btt509|pmid=24008419|pmc=3810854|issue=22}}</ref> <ref name="Tavaré 1986">{{cite journal |author=Tavaré S.|title= Some probabilistic and statistical problems in the analysis of DNA sequences. |journal=Lectures on Mathematics in the Life Sciences. American Mathematical Society|volume=17|pages=57–86|year=1986}}</ref> <ref name="Muse 1995">{{cite journal |author=Muse S. V. |title=Evolutionary analyses of DNA sequences subject to constraints of secondary structure.|journal=Genetics|volume=139 |issue=3 |pages=1429–1439|year=1995|doi=10.1093/genetics/139.3.1429|pmc=1206468 |pmid=7768450}}</ref> <ref name="Baker 1979">{{cite journal |doi=10.1121/1.2017061|title=Trainable grammars for speech recognition|journal=The Journal of the Acoustical Society of America|volume=65|issue=S1|pages=S132|year=1979|last1=Baker|first1=J. K.|bibcode=1979ASAJ...65Q.132B|doi-access=free}}</ref> <!-- <ref name="Myers 1995">{{cite journal |author=Myers, G.|title= Approximately matching context-free languages |journal=Information Processing Letters|volume=54|pages=85–92|year=1995|doi=10.1016/0020-0190(95)00007-Y}}</ref> --> <ref name="Schöniger 1994">{{cite journal |author1=Schöniger M. |author2=von Haeseler A. |title=A stochastic model for the evolution of autocorrelated DNA sequences |volume=3 |issue=3 |pages=240–7 |year=1994| journal = Mol. Phylogenet. Evol.|doi=10.1006/mpev.1994.1026|pmid=7529616 |bibcode=1994MolPE...3..240S }}</ref> }}
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