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Ivan Antonov et al.
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Daniel Lai et al.
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Goro Terai et al.
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Tanmoy Mondal et al.
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Aimin Li et al.
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Kevin V. Morris et al.
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Chenguang Gong et al.
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ViennaRNA Package 2.0
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Adaptive seeds tame genomic sequence comparison
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Chenguang Gong et al.
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RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming
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RNAstructure: software for RNA secondary structure prediction and analysis
Jessica S. Reuter et al.
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Prodigal: prokaryotic gene recognition and translation initiation site identification
Doug Hyatt et al.
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Genome-wide measurement of RNA secondary structure in yeast
Michael Kertesz et al.
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Piroon Jenjaroenpun et al.
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Jose Almeida Cruz et al.
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Mitchell Guttman et al.
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Ahmad M. Khalil et al.
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W Gerlach et al.
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The transcriptional landscape of the mammalian genome
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Searching genomes for sequences with the potential to form intrastrand triple helices
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