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FindPath specifications

Information


Unique identifier OMICS_04876
Name FindPath
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Stéphanie Heux

Publication for FindPath

FindPath citations

 (7)
library_books

A review of computational tools for design and reconstruction of metabolic pathways

2017
PMCID: 5851934
PMID: 29552648
DOI: 10.1016/j.synbio.2017.11.002

[…] method used to rank pathways is by the number of reaction steps, as this can be easily translated into an objective function in a number of methods (e.g., optstoic , cfp , and k-shortest efm , findpath ) to find the shortest pathway or pathway with the least total flux. the shortest pathway also implies fewest reaction steps or minimal enzyme requirement, thereby reducing […]

library_books

Tractable RNA–ligand interaction kinetics

2017
BMC Bioinformatics
PMCID: 5657077
PMID: 29072147
DOI: 10.1186/s12859-017-1823-5

[…] until one reaches structures within the already explored energy band. this approach seems to be more adequate in the context of a gradient basin coarse graining than a direct path heuristic (e. g. findpath [])., in step 2a, we compute the gradient basins and rates for the monomer landscape from the list of input structures using barriers [] (with minh heuristic). for step 2b, a list […]

library_books

A Max Flow Based Algorithm for Connected Target Coverage with Probabilistic Sensors

2017
PMCID: 5492299
PMID: 28587084
DOI: 10.3390/s17061208

[…] propose a bounded approximation algorithm 1, named the minimum vertices maximum flow algorithm (mvmfa). the key insight of mvmfa is that each augmenting path picked out by the pivotal algorithm 2 findpath has more flow and few inactive sensors. this means that a sensor with a high detection probability, but passing few relaying sensors by, will be activated firstly. our main contributions […]

library_books

Multi objective optimization for RNA design with multiple target secondary structures

2015
BMC Bioinformatics
PMCID: 4559319
PMID: 26335276
DOI: 10.1186/s12859-015-0706-x

[…] ensemble defect; cont: gc content. the str. column indicates whether the method assigns a predicted structure to each individual or not arnafold with option -p bwe use accessfindpath.py [] for the findpath.c [] in the vienna rna package cthe secondary structure of all nucleotide positions is constrained to obtain the free energy of a specified secondary structure like rnaeval dfree energy […]

library_books

Efficient path based computations on pedigree graphs with compact encodings

2012
BMC Bioinformatics
PMCID: 3311099
PMID: 22536898
DOI: 10.1186/1471-2105-13-S3-S14

[…] this way, we use the cpe code to recursively reconstruct all the non-tree paths. figure is the pseudo-code algorithm., example 4: let's take the node p6 in figure as an example and show how to use findpath algorithm in figure to find all paths from p1 to p6., p e t ( p 1 ) : 1 , c p e ( p 6 ) : 1 , 1 . $ 0 . 0 , 0 . $ 1 , 1 . # 1 , # 0 . 0 , # 1 , 0 . # 0 . 0 […]

library_books

Computing folding pathways between RNA secondary structures

2009
Nucleic Acids Res
PMCID: 2836545
PMID: 20044352
DOI: 10.1093/nar/gkp1054

[…] b is not too large. in (), flamm et al. describe a breadth-first search algorithm with bounded look-ahead, to compute nearly optimal ‘direct’ pathways. the algorithm is implemented in the program findpath.c, now part of the vienna rna package. finally, as part of the method parnass, voss et al. () describe a straightforward, greedy method to construct ‘direct’ pathways., our new algorithm, […]


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FindPath institution(s)
Université de Toulouse, Toulouse, France

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