GramCluster protocols

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GramCluster specifications

Information


Unique identifier OMICS_01956
Name GramCluster
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 1.3
Stability Stable
Maintained Yes

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  • person_outline GramAlign Team <>

Publication for GramCluster

GramCluster in pipeline

2013
PMCID: 3543377
PMID: 23326555
DOI: 10.1371/journal.pone.0053987

[…] other three thresholds assuming a linear relationship. rarefaction was calculated for reads pooled for all samples in mothur v1.21.1 . clusters delimited at these 6 grammatical threshold levels with gramcluster are available in . we also clustered forward sequences that were quality-trimmed, but not processed with ampliconnoise at 97% threshold to evaluate the effects of the data pruning step […]

GramCluster in publications

 (3)
PMCID: 3742672
PMID: 23967117
DOI: 10.1371/journal.pone.0070837

[…] corresponding cluster, otherwise a new cluster is created and the query sequence is stored as a new seed. based on a grammar distance metric, russell et al. proposed a sequence clustering algorithm gramcluster, which has a memory complexity of o(ln), where n is the number of sequences and l is the average sequence length. considering the computational efficiency and scalability, ghodsi et.al […]

PMCID: 3712477
PMID: 23534863
DOI: 10.1111/nph.12243

[…] fungal kingdom., an increasing number of clustering programs apply other similarity measures than absolute distances, relying on, for example, the grammatical structure of the sequence data (notably gramcluster by russell et al. (), crop by hao et al. (), and crunchclust by hartmann et al. ())., crunchclust, clotu, and scata are notable in offering a pyrosequencing homopolymer collapse option, […]

PMCID: 3543377
PMID: 23326555
DOI: 10.1371/journal.pone.0053987

[…] assignment. for the rarefaction analysis we clustered the remaining forward reads (including the ssu fragment, the its1, the 5.8s, and a fragment of the its2) with a grammar-based approach in gramcluster v1.3 . in this approach an alphabet is defined as a set of finite, nonempty symbols. these symbols form finite-length sequences, or strings. a language is considered as a subset […]

GramCluster institution(s)
Department of Electrical Engineering, University of Nebraska-Lincoln, Lincoln, NE, USA; Department of Food Science and Technology, University of Nebraska-Lincoln, Lincoln, NE, USA; Core for Applied Genomics and Ecology, University of Nebraska-Lincoln, Lincoln, NE, USA
GramCluster funding source(s)
National Institutes of Health (NIH)

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