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Path encoding specifications

Information


Unique identifier OMICS_07439
Name Path encoding
Alternative names kpath, PathEnc
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Version 0.6.3
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Carl Kingsford

Publication for Path encoding

Path encoding citations

 (13)
library_books

From chromatogram to analyte to metabolite. How to pick horses for courses from the massive web resources for mass spectral plant metabolomics

2017
GigaScience
PMCID: 5499862
PMID: 28520864
DOI: 10.1093/gigascience/gix037

[…] pathways of 28 different organisms. its interactive interface is similar to kegg, providing links with external resources for metabolites and enzymes. similarly, khaos metabolic pathways (kpath) [] is a database that integrates information related to metabolic pathways with 74 180 pathways, 13 153 reactions, and 37 029 metabolites providing tools for pathway visualization, editing, […]

library_books

Quantifying edge significance on maintaining global connectivity

2017
Sci Rep
PMCID: 5368568
PMID: 28349923
DOI: 10.1038/srep45380

[…] the possible source nodes, σsk(e) is the number of k-paths originating from s and traversing the edge e and, finally, σsk is the number of k-paths originating from s. for feasible application, erw-kpath(edge random walk k-path centrality) is adopted to efficiently compute edge centrality values. since the calculation of erw-kpath relies on random walks, it would be fine to fix k as high […]

library_books

Experimental Identification of Electric Field Excitation Mechanisms in a Structural Transition of Tokamak Plasmas

2016
Sci Rep
PMCID: 4973265
PMID: 27489128
DOI: 10.1038/srep30720

[…] wavenumber of turbulence kθ can be determined by the former setup. the radial wavenumber kr can be deduced from the poloidal wavenumber kθ and the wavenumber along the line of the sample volumes kpath, which is evaluated from the latter condition. the latter condition can also be used for the radial profile measurement, assuming that the plasma parameters such as the electrostatic potential […]

library_books

Whole genome sequencing targets drug resistant bacterial infections

2015
Hum Genomics
PMCID: 4525730
PMID: 26243131
DOI: 10.1186/s40246-015-0037-z

[…] interest []. in this case, wgs can act as a precursor to generate specific diagnostic tests for timely case definition [, , ]. the genomic data should be analyzed using computational methods (e.g., kpath, tofi, insignia, topsi, ssgenefinder, or alignment-free methods) in order to identify pathogen signatures, estimate their evolutionary rates across the group, and design highly specific […]

library_books

Comparative study of the protein profiles of Sunki mandarin and Rangpur lime plants in response to water deficit

2015
BMC Plant Biol
PMCID: 4355367
PMID: 25849288
DOI: 10.1186/s12870-015-0416-6

[…] furthermore, non-hub/bottleneck (nh-b) nodes were also identified due to the essential nature of the bottleneck nodes in the network dynamics., edge centrality analysis was performed using the werw-kpath algorithm [], and data input generation was added as a network attribute in cytoscape 2.8.2. in addition, quantitative protein expression data were distributed in the protein interaction […]

library_books

Cell Fate Regulation Governed by a Repurposed Bacterial Histidine Kinase

2014
PLoS Biol
PMCID: 4211667
PMID: 25349992
DOI: 10.1371/journal.pbio.1001979

[…] of protein, and absorbance at 340 nm was recorded every 10 seconds for a 30 minute period. the slope of a stable linear absorbance decay was measured to calculate atp hydrolysis rates, using a nadh kpath value of 3,248 od m−1 . background rates of atp hydrolysis and nadh oxidation were measured and subtracted from observed atp hydrolysis rates of all divl constructs., ccka(70–691) […]


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Path encoding institution(s)
Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA; Department of Computer Science, Stony Brook University, Stony Brook, NY, USA
Path encoding funding source(s)
Supported by the Gordon and Betty Moore Foundation’s Data-Driven Discovery Initiative through Grant GBMF4554, the US National Science Foundation [grant numbers CCF-1256087, CCF-1319998], US National Institutes of Health [R21HG006913, R01HG007104] and Alfred P. Sloan Research Fellow.

Path encoding review

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Anonymous user #383

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Desktop
This tool is indeed very efficient in compressing fastq files.
Unfortunately in the compressed file you lose all info in the sequence identifier and the quality score.