Cargando…

WordCluster: detecting clusters of DNA words and genomic elements

BACKGROUND: Many k-mers (or DNA words) and genomic elements are known to be spatially clustered in the genome. Well established examples are the genes, TFBSs, CpG dinucleotides, microRNA genes and ultra-conserved non-coding regions. Currently, no algorithm exists to find these clusters in a statisti...

Descripción completa

Detalles Bibliográficos
Autores principales:	Hackenberg, Michael, Carpena, Pedro, Bernaola-Galván, Pedro, Barturen, Guillermo, Alganza, Ángel M, Oliver, José L
Formato:	Texto
Lenguaje:	English
Publicado:	BioMed Central 2011
Materias:	Software Article
Acceso en línea:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3037320/ https://www.ncbi.nlm.nih.gov/pubmed/21261981 http://dx.doi.org/10.1186/1748-7188-6-2

Ejemplares similares

NGSmethDB 2017: enhanced methylomes and differential methylation
por: Lebrón, Ricardo, et al.
Publicado: (2017)

Phylogenetic distribution of large-scale genome patchiness
por: Oliver, José L, et al.
Publicado: (2008)

Prediction of CpG-island function: CpG clustering vs. sliding-window methods
por: Hackenberg, Michael, et al.
Publicado: (2010)

NGSmethDB: an updated genome resource for high quality, single-cytosine resolution methylomes
por: Geisen, Stefanie, et al.
Publicado: (2014)

BioWord: A sequence manipulation suite for Microsoft Word
por: Anzaldi, Laura J, et al.
Publicado: (2012)

Compositional Structure of the Genome: A Review
por: Bernaola-Galván, Pedro, et al.
Publicado: (2023)

sRNAtoolbox: an integrated collection of small RNA research tools
por: Rueda, Antonio, et al.
Publicado: (2015)

Word add-in for ontology recognition: semantic enrichment of scientific literature
por: Fink, J Lynn, et al.
Publicado: (2010)

ClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements
por: Ozer, Egon A.
Publicado: (2018)

The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes through oligonucleotide usage
por: Ganesan, Hamilton, et al.
Publicado: (2008)

Rapid publication-ready MS-Word tables for one-way ANOVA
por: Assaad, Houssein I, et al.
Publicado: (2014)

Rapid publication-ready MS-Word tables for two-way ANOVA
por: Assaad, Houssein I, et al.
Publicado: (2015)

Changing word meanings in biomedical literature reveal pandemics and new technologies
por: Nicholson, David N., et al.
Publicado: (2023)

SweepCluster: A SNP clustering tool for detecting gene-specific sweeps in prokaryotes
por: Qiu, Junhui, et al.
Publicado: (2022)

Distinguishing Functional DNA Words; A Method for Measuring Clustering Levels
por: Moghaddasi, Hanieh, et al.
Publicado: (2017)

The influence of clustering coefficient on word-learning: how groups of similar sounding words facilitate acquisition
por: Goldstein, Rutherford, et al.
Publicado: (2014)

On the Validity of Detrended Fluctuation Analysis at Short Scales
por: Carpena, Pedro, et al.
Publicado: (2021)

The High Throughput Sequence Annotation Service (HT-SAS) – the shortcut from sequence to true Medline words
por: Kaczanowski, Szymon, et al.
Publicado: (2009)

Words, Words, Words
por: Sreenivasan, T
Publicado: (2011)

Words, words, words
por: Van Oyen, H, et al.
Publicado: (2011)

Words, Words, Words
Publicado: (1900)

clusterMaker: a multi-algorithm clustering plugin for Cytoscape
por: Morris, John H, et al.
Publicado: (2011)

optCluster: An R Package for Determining the Optimal Clustering Algorithm
por: Sekula, Michael, et al.
Publicado: (2017)

clusterMaker2: a major update to clusterMaker, a multi-algorithm clustering app for Cytoscape
por: Utriainen, Maija, et al.
Publicado: (2023)

PSE: A tool for browsing a large amount of MEDLINE/PubMed abstracts with gene names and common words as the keywords
por: Yoneya, Takashi
Publicado: (2005)

MotifCluster: an interactive online tool for clustering and visualizing sequences using shared motifs
por: Hamady, Micah, et al.
Publicado: (2008)

The word detective
por: Morris, Evan
Publicado: (2000)

Defining a Conceptual Topography of Word Concreteness: Clustering Properties of Emotion, Sensation, and Magnitude among 750 English Words
por: Troche, Joshua, et al.
Publicado: (2017)

LeARN: a platform for detecting, clustering and annotating non-coding RNAs
por: Noirot, Céline, et al.
Publicado: (2008)

ICGE: an R package for detecting relevant clusters and atypical units in gene expression
por: Irigoien, Itziar, et al.
Publicado: (2012)

Words, more words and nothing but words???
por: Association du personnel
Publicado: (2006)

Automated analysis of phylogenetic clusters
por: Ragonnet-Cronin, Manon, et al.
Publicado: (2013)

proTRAC - a software for probabilistic piRNA cluster detection, visualization and analysis
por: Rosenkranz, David, et al.
Publicado: (2012)

CAGECAT: The CompArative GEne Cluster Analysis Toolbox for rapid search and visualisation of homologous gene clusters
por: van den Belt, Matthias, et al.
Publicado: (2023)

NGSmethDB: a database for next-generation sequencing single-cytosine-resolution DNA methylation data
por: Hackenberg, Michael, et al.
Publicado: (2011)

Combinatorics on words: Christoffel words and repetitions in words
por: Berstel, Jean, et al.
Publicado: (2008)

Cnidaria: fast, reference-free clustering of raw and assembled genome and transcriptome NGS data
por: Aflitos, Saulo Alves, et al.
Publicado: (2015)

fcScan: a versatile tool to cluster combinations of sites using genomic coordinates
por: El-Kurdi, Abdullah, et al.
Publicado: (2020)

Identifying Clusters of Rare and Novel Words in Emergency Department Chief Complaints
por: Walsh, Andrew, et al.
Publicado: (2014)

Long-Range Memory in Literary Texts: On the Universal Clustering of the Rare Words
por: Tanaka-Ishii, Kumiko, et al.
Publicado: (2016)

Cannot write session to /tmp/vufind_sessions/sess_0i6f3ig5eb1bfa8pu77fan529d