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Consan specifications


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


No version available


  • person_outline Robin Dowell

Publication for Consan

Consan citations


Detecting and Comparing Non Coding RNAs in the High Throughput Era

Int J Mol Sci
PMCID: 3759867
PMID: 23887659
DOI: 10.3390/ijms140815423

[…] 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 […]


From Structure Prediction to Genomic Screens for Novel Non Coding RNAs

PLoS Comput Biol
PMCID: 3150283
PMID: 21829340
DOI: 10.1371/journal.pcbi.1002100

[…] 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 […]


BlastR—fast and accurate database searches for non coding RNAs

Nucleic Acids Res
PMCID: 3167602
PMID: 21624887
DOI: 10.1093/nar/gkr335

[…] 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 […]


ModeRNA: a tool for comparative modeling of RNA 3D structure

Nucleic Acids Res
PMCID: 3105415
PMID: 21300639
DOI: 10.1093/nar/gkq1320

[…] 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 […]


Hidden Markov Models and their Applications in Biological Sequence Analysis

Curr Genomics
PMCID: 2766791
PMID: 20190955
DOI: 10.2174/138920209789177575

[…] 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 […]


Evolutionary Triplet Models of Structured RNA

PLoS Comput Biol
PMCID: 2725318
PMID: 19714212
DOI: 10.1371/journal.pcbi.1000483

[…] 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 ( […]


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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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