PMC:1892782 / 2301-3325 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1892782","sourcedb":"PMC","sourceid":"1892782","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1892782","text":"Small differences in the measured folding energies between an RNA molecule and its reverse complement are captured by corresponding small asymmetries in the standard energy model used by thermodynamic folding algorithms [9,10]. These differences distinguish the two reading directions even in the absence of GU pairs. In addition, GU pairs have an asymmetric effect in multiple sequence alignments: Suppose a particular pair of alignment columns exhibits a GC → GU substitution in one reading direction; this preserves base pairing and hence is consistent with a conserved structure. The reverse complement of the same alignment, however, displays a GC → AC substitution which is inconsistent with a conserved base pair. The patterns of structure conservation, and hence the consensus structure and its associated average folding energy, as computed by the RNAalifold algorithm [11], thus differ between the reading directions. In contrast, compensatory mutations, such as GC → AU do not provide strand-specific information.","tracks":[{"project":"2_test","denotations":[{"id":"17540014-10329189-1690042","span":{"begin":221,"end":222},"obj":"10329189"},{"id":"17540014-16982646-1690043","span":{"begin":223,"end":225},"obj":"16982646"},{"id":"17540014-12079347-1690044","span":{"begin":879,"end":881},"obj":"12079347"}],"attributes":[{"subj":"17540014-10329189-1690042","pred":"source","obj":"2_test"},{"subj":"17540014-16982646-1690043","pred":"source","obj":"2_test"},{"subj":"17540014-12079347-1690044","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#c7ec93","default":true}]}]}}