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Protocols

SPHINX specifications

Information


Unique identifier OMICS_01466
Name SPHINX
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No

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Publication for SPHINX

SPHINX citations

 (3)
library_books

Bioinformatic approaches for functional annotation and pathway inference in metagenomics data

2012
Brief Bioinform
PMCID: 3505041
PMID: 23175748
DOI: 10.1093/bib/bbs070

[…] s are MEGAN [], CARMA [], Sort-ITEMS [] or MetaPhyler [] that use similarity searches, the faster PhyloPythia [] or TETRA [] that use taxonomy-fitted nucleotide or codon usage composition analysis or SPHINX that uses a combination of the two [].A number of models have already been published [] by integrating known interactions (e.g. reagent/product at the enzyme level) from pathway repositories su […]

library_books

A comparative evaluation of sequence classification programs

2012
BMC Bioinformatics
PMCID: 3428669
PMID: 22574964
DOI: 10.1186/1471-2105-13-92

[…] r more so than when using other methods.Programs that primarily utilize sequence composition models include Naive Bayes Classifier (NBC) [,], PhyloPythia [,], PhymmBL [], RAIphy [], RDP [], Scimm [], SPHINX [], and TACOA []. Methods for building sequence models often make use of interpolated Markov models (IMMs), naive Bayesian classifiers, and k-means/k-nearest-neighbor algorithms. There is some […]

call_split

Metagenome of the gut of a malnourished child

2011
PMCID: 3115890
PMID: 21599906
DOI: 10.1186/1757-4749-3-7
call_split See protocol

[…] nces having at least 80% identity (spread over at least 80% of the length) to human sequences were removed from subsequent analyses.All reads in both data sets were taxonomically classified using the SPHINX algorithm []. Analysis of these assignments at various taxonomic levels was performed by first collapsing all assignments at a desired taxonomic level, and subsequently enumerating the number o […]


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SPHINX institution(s)
Bio-sciences R&D Division, TCS Innovation Labs, Tata Consultancy Services Limited, Madhapur, Hyderabad, Andhra Pradesh, India

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