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Inferring Noncoding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering[J] Sebastian Will;Kristin Reiche;Ivo L Hofacker;Peter F Stadler;Rolf Backofen PLOS Computational Biology 2007,
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Multiple Sequence Alignment with Evolutionary Computation.[J] Conrad Shyu;Luke Sheneman;James A. Foster Genetic Programming and Evolvable Machines 2004,
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Consensus Folding of Aligned Sequences as a New Measure for the Detection of Functional RNAs by Comparative Genomics[J] Stefan Washietl;Ivo L. Hofacker Journal of Molecular Biology 2004,
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RNA-based phylogenetic methods: application to mammalian mitochondrial RNA sequences[J] Cendrine Hudelot;Vivek Gowri-Shankar;Howsun Jow;Magnus Rattray;Paul G Higgs Molecular Phylogenetics and Evolution 2003,
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Secondary Structure Prediction for Aligned RNA Sequences[J] Ivo L. Hofacker;Martin Fekete;Peter F. Stadler Journal of Molecular Biology 2002,
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Dynalign: an algorithm for finding the secondary structure common to two RNA sequences 1 1 Edited by I. Tinoco[J] David H. Mathews;Douglas H. Turner Journal of Molecular Biology 2002,
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SQUID-C function library for sequence analysis Eddy S; http://www.genetics.wustl.edu/eddy/software/#squid 2004,