Consan

[…] the same dataset that was utilized in benchmarking experiments performed in a previous paper (), so results are directly comparable with previous benchmarks on dynalign (), foldalign (), stemloc (), consan (), locarna () and single sequence structure prediction based on free energy minimization (). the cluster analysis was performed on the generated sample of structures and sequence alignments […]

[…] use a subset of the free energy nearest neighbor parameters []. the revised foldalign restricts the alignment space to reduce runtime. two scfg-based programs are available, stemloc package [,] and consan []. to reduce runtime, stemloc introduced the concept of fold and alignment envelopes that restrict, respectively, the search space for possible base pairs and possible nucleotide alignments. […]

[…] constraint) [] were also compared against three other dynamic programming algorithms. the three other programs are foldalign [], which uses a free energy-based scoring function, and stemloc [] and consan [], which use scfg models. each program was run using default parameters. our interest is both in the accuracy of the methods and in their use of resources, cpu time and memory., tables and […]

[…] mas = macrophage activation syndrome, dada = deficiency of adenosine deaminase, caps = cryopyrin-associated autoinflammatory syndromes, crmo = chronic recurrent multifocal osteomyelitis, consan = consanguinity (y = yes, n = no, u = unknown), sex (f = female, m = male). hsct = haematopoietic stem cell transplantation, cs = corticosteroid (including pulses of intravenous […]

[…] a further detailed examination of the case. a provisional diagnosis of apert's syndrome was established, and detailed examination has been carried out., the boy was fourth in the family born to non-consan­guineous parents after the normal labor. the birth history of the patient was uneventful with no known exposure to infection, drugs or irradiation during his mother's pregnancy. no similar […]

[…] 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 […]

[…] 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 […]

[…] 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 […]