Consan

[…] 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 […]

[…] 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 […]