PatternBranching/ProfileBranching statistics

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PatternBranching/ProfileBranching specifications

Information


Unique identifier OMICS_21809
Name PatternBranching/ProfileBranching
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Subtools


  • Pattern Branching
  • ProfileBranching

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Maintainer


  • person_outline Alkes Price <>

Publication for PatternBranching/ProfileBranching

PatternBranching/ProfileBranching in publications

 (4)
PMCID: 4299504
PMID: 25292187
DOI: 10.1111/joa.12239

[…] the fact that not all nodes retract simultaneously suggests that the phenomenon cannot be triggered solely by a global, organ-wide signal. cebri├ín et al. () noted that the transition from early-pattern branching to having long medullary ducts coincided with differentiation of the stroma, and pointed out that mutants that inhibit stromal development have an abnormally shallow medulla. […]

PMCID: 4022013
PMID: 24555784
DOI: 10.1186/1745-6150-9-4

[…] of the sequences. the best consensus with highest score is chosen to describe the motifs in the sequences []., some examples of consensus-based algorithms are winnower [], consensus [], and profilebranching []., this approach solves the (l, k) motif problem where each instance of a motif of length l differs from the original motif by exactly k positions. these k positions are used […]

PMCID: 3063805
PMID: 21385438
DOI: 10.1186/1756-0500-4-54

[…] there is no guarantee that we will get all the motifs of interest. other examples of approximate algorithms include: multiprofiler [], patternbranching [], consensus [], gibbsdna [], meme [], and profilebranching []., several exact algorithms are also known for solving the pms problem: [-], and []. pms algorithms are typically tested on random benchmark data generated as follows: twenty […]

PMCID: 1687185
PMID: 17129371
DOI: 10.1186/1748-7188-1-23

[…] is that consensus patterns are not as expressive of the dna signal as profile representations. recent approaches within this framework include projection methods [,], string based methods [], pattern-branching [], multiprofiler [] and other branch and bound approaches [,]., a hybrid approach could potentially combine the expressiveness of the profile representation with convergence […]


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PatternBranching/ProfileBranching institution(s)
Department of Computer Science and Engineering, University of California at San Diego, La Jolla, CA, USA

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