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.
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