Author: Seemann, Stefan E.; Gorodkin, Jan; Backofen, Rolf
Title: Unifying evolutionary and thermodynamic information for RNA folding of multiple alignments Document date: 2008_10_4
ID: wtvfow2f_37
Snippet: where P t is the number of mutual base pairs in the two assignments (true positives), N t the number of mutual pairs of bases not base pairing (true negatives), P f the number of predicted base pairs not in the Rfam assignment (false positives) and N f the number of base pairs in the Rfam assignment not predicted to pair (false negatives). We also calculated sensitivity, SEN ¼ P t =ðP t þ N f Þ and positive predictive value, PPV ¼ P t =ðP t.....
Document: where P t is the number of mutual base pairs in the two assignments (true positives), N t the number of mutual pairs of bases not base pairing (true negatives), P f the number of predicted base pairs not in the Rfam assignment (false positives) and N f the number of base pairs in the Rfam assignment not predicted to pair (false negatives). We also calculated sensitivity, SEN ¼ P t =ðP t þ N f Þ and positive predictive value, PPV ¼ P t =ðP t þ P f Þ. Their geometric mean is a good approximation to the MCC for base pair prediction (43) . The parameter tuning was done by optimizing the MCC to get a best possible tradeoff between sensitivity and PPV. In addition, we used the more stringent structure evaluation scheme R 5 introduced by Gorodkin et al.
Search related documents:
Co phrase search for related documents- base pair and parameter tuning: 1, 2, 3
- base pair prediction and parameter tuning: 1
- false negative and positive predictive value: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41
- false negative and PPV sensitivity: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13
- false negative and predictive value: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60
- false negative and true negative: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70
- false negative and true positive: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56
- false positive and geometric mean: 1
Co phrase search for related documents, hyperlinks ordered by date