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_3
Snippet: Hence, it is desirable to combine this duality of RNA structure information into a single optimization problem. This was probably addressed for the first time in 1985 by David Sankoff (7) , who introduced an algorithm that solved the problem of simultaneously aligning and folding a set of unaligned RNA sequences. While, this is a kind of gold standard for comparative RNA secondary structure prediction, the 'algorithm requires extreme amounts of m.....
Document: Hence, it is desirable to combine this duality of RNA structure information into a single optimization problem. This was probably addressed for the first time in 1985 by David Sankoff (7) , who introduced an algorithm that solved the problem of simultaneously aligning and folding a set of unaligned RNA sequences. While, this is a kind of gold standard for comparative RNA secondary structure prediction, the 'algorithm requires extreme amounts of memory and time' (8) . Thus, practical implementations of the Sankoff algorithm like FOLDALIGN (9-12), Dynalign (13, 14) , PMcomp (15) , LocARNA (16, 17) and PARTS (18) , published more than 20 years later, introduce different constraints and somewhat arbitrary choices in their scoring schemes to make the approach tractable for realistic input sizes.
Search related documents:
Co phrase search for related documents- RNA secondary structure prediction and secondary structure prediction: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24
- RNA sequence and Sankoff algorithm: 1
- RNA sequence and secondary structure: 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
- RNA sequence and secondary structure prediction: 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11
- RNA sequence and structure information: 1, 2, 3, 4, 5, 6, 7, 8, 9
- RNA structure information and secondary structure: 1, 2, 3, 4, 5, 6
- RNA structure information and structure information: 1, 2, 3, 4, 5, 6, 7, 8, 9
- RNA structure information duality and secondary structure: 1
- RNA structure information duality and structure information: 1
- secondary structure and single optimization problem: 1
- secondary structure and structure information: 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
- secondary structure prediction and structure information: 1
Co phrase search for related documents, hyperlinks ordered by date