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Protocols

Consan specifications

Information


Unique identifier OMICS_11353
Name Consan
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.2
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Robin Dowell <>

Publication for Consan

Consan citations

 (12)
library_books

Clinical impact of a targeted next generation sequencing gene panel for autoinflammation and vasculitis

2017
PMCID: 5531484
PMID: 28750028
DOI: 10.1371/journal.pone.0181874

[…] 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 […]

library_books

Apert's Syndrome

2014
PMCID: 4144061
PMID: 25206244
DOI: 10.5005/jp-journals-10005-1239

[…] 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 […]

library_books

Detecting and Comparing Non Coding RNAs in the High Throughput Era

2013
PMCID: 3759867
PMID: 23887659
DOI: 10.3390/ijms140815423

[…] 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 […]

library_books

From Structure Prediction to Genomic Screens for Novel Non Coding RNAs

2011
PMCID: 3150283
PMID: 21829340
DOI: 10.1371/journal.pcbi.1002100

[…] 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 […]

library_books

Hidden Markov Models and their Applications in Biological Sequence Analysis

2009
PMCID: 2766791
PMID: 20190955
DOI: 10.2174/138920209789177575

[…] 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 […]

library_books

Evolutionary Triplet Models of Structured RNA

2009
PMCID: 2725318
PMID: 19714212
DOI: 10.1371/journal.pcbi.1000483

[…] 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 […]


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Consan institution(s)
Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, St Louis, MO, USA; MIT Computer Science and Artificial Intelligence Laboratory, Cambridge, MA, USA

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