Describing the Structural Diversity within an RNA’s Ensemble
RNA is usually classified as either structured or unstructured; however, neither category is adequate in describing the diversity of secondary structures expected in biological systems We describe this diversity within the ensemble of structures by using two different metrics: the average Shannon en...
| Main Author: | |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2014-03-01
|
| Series: | Entropy |
| Subjects: | |
| Online Access: | http://www.mdpi.com/1099-4300/16/3/1331 |
| _version_ | 1811306799455797248 |
|---|---|
| author | Joshua S. Martin |
| author_facet | Joshua S. Martin |
| author_sort | Joshua S. Martin |
| collection | DOAJ |
| description | RNA is usually classified as either structured or unstructured; however, neither category is adequate in describing the diversity of secondary structures expected in biological systems We describe this diversity within the ensemble of structures by using two different metrics: the average Shannon entropy and the ensemble defect. The average Shannon entropy is a measure of the structural diversity calculated from the base pair probability matrix. The ensemble defect, a tool in identifying optimal sequences for a given structure, is a measure of the average number of structural differences between a target structure and all the structures that make up the ensemble, scaled to the length of the sequence. In this paper, we show examples and discuss various uses of these metrics in both structured and unstructured RNA. By exploring how these two metrics describe RNA as an ensemble of different structures, as would be found in biological systems, it will push the field beyond the standard “structured” and “unstructured” categorization. |
| first_indexed | 2024-04-13T08:52:12Z |
| format | Article |
| id | doaj.art-59f9dda6da6148eb84f75fbd54db815a |
| institution | Directory Open Access Journal |
| issn | 1099-4300 |
| language | English |
| last_indexed | 2024-04-13T08:52:12Z |
| publishDate | 2014-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Entropy |
| spelling | doaj.art-59f9dda6da6148eb84f75fbd54db815a2022-12-22T02:53:26ZengMDPI AGEntropy1099-43002014-03-011631331134810.3390/e16031331e16031331Describing the Structural Diversity within an RNA’s EnsembleJoshua S. Martin0National Evolutionary Synthesis Center, Durham, NC 27705, USARNA is usually classified as either structured or unstructured; however, neither category is adequate in describing the diversity of secondary structures expected in biological systems We describe this diversity within the ensemble of structures by using two different metrics: the average Shannon entropy and the ensemble defect. The average Shannon entropy is a measure of the structural diversity calculated from the base pair probability matrix. The ensemble defect, a tool in identifying optimal sequences for a given structure, is a measure of the average number of structural differences between a target structure and all the structures that make up the ensemble, scaled to the length of the sequence. In this paper, we show examples and discuss various uses of these metrics in both structured and unstructured RNA. By exploring how these two metrics describe RNA as an ensemble of different structures, as would be found in biological systems, it will push the field beyond the standard “structured” and “unstructured” categorization.http://www.mdpi.com/1099-4300/16/3/1331secondary structureensemble of structuressingle nucleotide polymorphismsribosome |
| spellingShingle | Joshua S. Martin Describing the Structural Diversity within an RNA’s Ensemble Entropy secondary structure ensemble of structures single nucleotide polymorphisms ribosome |
| title | Describing the Structural Diversity within an RNA’s Ensemble |
| title_full | Describing the Structural Diversity within an RNA’s Ensemble |
| title_fullStr | Describing the Structural Diversity within an RNA’s Ensemble |
| title_full_unstemmed | Describing the Structural Diversity within an RNA’s Ensemble |
| title_short | Describing the Structural Diversity within an RNA’s Ensemble |
| title_sort | describing the structural diversity within an rna s ensemble |
| topic | secondary structure ensemble of structures single nucleotide polymorphisms ribosome |
| url | http://www.mdpi.com/1099-4300/16/3/1331 |
| work_keys_str_mv | AT joshuasmartin describingthestructuraldiversitywithinanrnasensemble |