Consan

[…] the times and calls for simplified heuristics. Several banded modifications of the Sankoff algorithm impose limits on the size or shape of substructures, like Dynalign [,], Foldalign [,], Stemloc [], Consan []. Another example is pmmulti [], a Sankoff algorithm variant able to perform multiple secondary structure alignments by aligning consensus base pair probability matrices. Plan C is used by pr […]

[…] structures only. Later, more complete versions were published and the first full-scale implementation for two sequences was dynalign , . A nice SCFG framework was also introduced in stemloc and later consan methods –. Later, PMcomp and LocARNA introduced the use of pre-computed base pair probability matrices to reduce computational cost (PMcomp) and memory (LocARNA). Common for these methods is […]

[…] of sequences and L their length] and their practical usage requires the design of heuristic versions with lower complexity. These include Genetic Algorithms () or banded Sankoff implementations like Consan (). In practice, however, the most popular applications to perform efficient database searches make use of stochastic context free grammars (SCFG) (). These include Rsearch () and RaveNna () th […]

[…] RNA sequence alignment. There are programs utilizing either sequence information alone like Muscle () or ClustalW (), as well as methods that combine sequence and secondary-structure information like Consan () for pairwise alignments, or LocARNA (), FoldalignM () or Stemloc () for multiple alignments. A more comprehensive list of available tools is discussed in the article describing the R-Coffee […]

[…] approach can be used to speed up profile-csHMM based RNA searches [].There also exist a number of methods to improve the speed of simultaneous RNA folding and alignment algorithms [, ]. For example, Consan implements a constrained version of the pairwise RNA structure prediction and alignment algorithm based on pair stochastic context-free grammars (pair-SCFGs) []. It assumes the knowledge of a f […]

[…] gnment, or a relatively small set of candidate alignments (as in the ORTHEUS program ). Such constraints are commonly used by programs for SCFG-based RNA sequence analysis such as QRNA , Stemloc and CONSAN . Alignment and structural constraints can be combined .In the following sections we introduce more precise definitions for two-sequence models of RNA structure and outline our algorithms for ( […]