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Rapid hierarchical clustering of biological sequences

Timothy Chappell, Shlomo Geva, James Hogan, Dimitri Perrin
2018 Proceedings of the 23rd Australasian Document Computing Symposium on ZZZ - ADCS '18  
Rapid hierarchical clustering of biological sequences. In 23rd Australasian Document Computing Symposium (ADCS '18), December 11-12, 2018, Dunedin, New Zealand.  ...  METHODS The contribution of this paper is to provide rapid and accurate clustering of sequence datasets at very large scale, markedly extending the range of problems which may be analysed in a convenient  ... 
doi:10.1145/3291992.3291998 dblp:conf/adcs/ChappellGHP18 fatcat:aowdsqcvirholl7566uvrgggya

Typing of Nosocomial Outbreaks of Acinetobacter baumannii by Use of Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry

A. Mencacci, C. Monari, C. Leli, L. Merlini, E. De Carolis, A. Vella, M. Cacioni, S. Buzi, E. Nardelli, F. Bistoni, M. Sanguinetti, A. Vecchiarelli
2012 Journal of Clinical Microbiology  
in comparison with the repetitive sequence-based PCR DiversiLab system.  ...  Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) has been evaluated for the identification of multidrug-resistant Acinetobacter baumannii nosocomial outbreaks  ...  (B) Dendrogram representation of hierarchical cluster analysis provided by MALDI-TOF MS.  ... 
doi:10.1128/jcm.01811-12 pmid:23175257 pmcid:PMC3553918 fatcat:o74ybu6rb5c5lkhbgun6iyjqou

CIT: A Cluster Identification Tool based on Biclustering and Hierarchical Clustering

Tabinda Hussain, Ammara Mazhar, Ammad-ud-din, Asif Mir
2009 Journal of Proteomics & Bioinformatics  
With this project work, we have developed a cluster identifying tool, i.e. CIT which is based on two different clustering methodologies namely; Biclustering and Hierarchical Clustering.  ...  With such modern technologies, it has now become easier to find practical manifestations of microarray data in the fields of pharmacogenomics, cancer genetics and biological network construction.  ...  Background Rapid advances in genome-scale sequencing has led to immense increase in the amount of biological information .Simply visualizing this kind of data which is widely called gene expression data  ... 
doi:10.4172/jpb.1000080 fatcat:yh4ycywpgrhp7pn7ktimtqv5yi

Using Global Sequence Similarity to Enhance Biological Sequence Labeling

Cornelia Caragea, Jivko Sinapov, Drena Dobbs, Vasant Honavar
2008 2008 IEEE International Conference on Bioinformatics and Biomedicine  
Given a set of sequences and a similarity measure defined on pairs of sequences, we learn a mixture of experts model by using spectral clustering to learn the hierarchical structure of the model and by  ...  The results of our experiments show that global sequence similarity can be exploited to improve the performance of classifiers trained to label biological sequence data.  ...  Introduction Advances in high throughput data acquisition technologies have resulted in rapid increase in the amount of data in biological sciences.  ... 
doi:10.1109/bibm.2008.54 dblp:conf/bibm/CarageaSDH08 fatcat:42q7rgmelnb2hbe4lycufvu3iy

Functional annotation prediction: All for one and one for all

Ori Sasson, Noam Kaplan, Michal Linial
2006 Protein Science  
In an era of rapid genome sequencing and high-throughput technology, automatic function prediction for a novel sequence is of utter importance in bioinformatics.  ...  ProtoNet is a hierarchical organization of the protein sequences in the UniProt database.  ...  Acknowledgments Special thanks to the ProtoNet team for support at all stages of ProtoNet development.  ... 
doi:10.1110/ps.062185706 pmid:16672244 pmcid:PMC2242553 fatcat:invabbcwcfb5rlgzfvv7kzkx3q

An novel frequent probability pattern mining algorithm based on circuit simulation method in uncertain biological networks

Jieyue He, Chunyan Wang, Kunpu Qiu, Wei Zhong
2014 BMC Systems Biology  
Finally, based on the algorithm of probability subgraph isomorphism, two-step hierarchical clustering method is used to cluster subgraphs, and discover frequent probability patterns from the clusters.  ...  Most of current research on biological networks focuses on exact motif mining.  ...  An earlier version of this article was published for the IEEE International Conference on Bioinformatics and Biomedicine (BIBM) held on December 18-21, 2013 [34] .  ... 
doi:10.1186/1752-0509-8-s3-s6 pmid:25350277 pmcid:PMC4243085 fatcat:zurgajtmazdfzhkdg2yc4bpahy

A map of the protein space--an automatic hierarchical classification of all protein sequences

G Yona, N Linial, N Tishby, M Linial
1998 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
The hierarchical organization proposed may be considered as the first map of the space of all protein sequences.  ...  This graph encodes much of the fundamental properties of the sequence space. We look for clusters of related proteins in this graph. These clusters correspond to strongly connected sets of vertices.  ...  We seek clusters of related sequences which can be assigned a characteristic biological function.  ... 
pmid:9783227 fatcat:qvmwke63kzdwjaalrsb7zfwnva

ORIO (Online Resource for Integrative Omics): a web-based platform for rapid integration of next generation sequencing data

Christopher A. Lavender, Andrew J. Shapiro, Adam B. Burkholder, Brian D. Bennett, Karen Adelman, David C. Fargo
2017 Nucleic Acids Research  
Established and emerging next generation sequencing (NGS)-based technologies allow for genomewide interrogation of diverse biological processes.  ...  Data are then integrated using clustering-based approaches, giving hierarchical relationships across NGS datasets and separating individual genomic features into groups.  ...  We thank Paul Wade, Guang Hu, and Jason Li for critical comments during review of the manuscript.  ... 
doi:10.1093/nar/gkx270 pmid:28402545 pmcid:PMC5449597 fatcat:7sn7bqiqkbdvvbgoyexr2v2mfi

VisHiC--hierarchical functional enrichment analysis of microarray data

D. Krushevskaya, H. Peterson, J. Reimand, M. Kull, J. Vilo
2009 Nucleic Acids Research  
We present VisHiC (Visualization of Hierarchical Clustering), a web server for clustering and compact visualization of gene expression data combined with automated function enrichment analysis.  ...  The main output of the analysis is a dendrogram and visual heatmap of the expression matrix that highlights biologically relevant clusters based on enriched GO terms, pathways and regulatory motifs.  ...  J.R. and M.K. acknowledge the Tiger University Program of the Estonian Information Technology Foundation.  ... 
doi:10.1093/nar/gkp435 pmid:19483095 pmcid:PMC2703939 fatcat:xojh6d5dsvhppd55odbaxgvpry

Public databases and software for the pathway analysis of cancer genomes

Ivy F L Tsui, Raj Chari, Timon P H Buys, Wan L Lam
2007 Cancer Informatics  
The study of pathway disruption is key to understanding cancer biology. Advances in high throughput technologies have led to the rapid accumulation of genomic data.  ...  In this review, we discuss approaches to the analysis of genomic data and describe the publicly available resources for studying biological pathways.  ...  Graphical output display of heatmap, hierarchical clustering, and principal component analysis.  ... 
pmid:19455256 pmcid:PMC2410087 fatcat:xb36gu4llvfzfpjyxn4bls4dsq

MBGD update 2018: microbial genome database based on hierarchical orthology relations covering closely related and distantly related comparisons

Ikuo Uchiyama, Motohiro Mihara, Hiroyo Nishide, Hirokazu Chiba, Masaki Kato
2018 Nucleic Acids Research  
a phylogenetic tree of each taxon based on the concatenated core gene sequences.  ...  In addition, we have enhanced several functionalities, including rapid and flexible keyword searching, profile-based sequence searching for orthology assignment to a user query sequence, and displaying  ...  In particular, MMseqs2 is rapid enough to search the profile library even with a complete set of protein sequences in a bacterial genome as a query.  ... 
doi:10.1093/nar/gky1054 pmid:30462302 pmcid:PMC6324027 fatcat:xo4ckwyetvffng3uztkfhhqosq

Interactive color mosaic and dendrogram displays for signal/noise optimization in microarray data analysis

Jinwook Seo, M. Bakay, Po Zhao, Yi-Wen Chen, P. Clarkson, B. Shneiderman, E.P. Hoffman
2003 2003 International Conference on Multimedia and Expo. ICME '03. Proceedings (Cat. No.03TH8698)  
" biological groups (unsupervised clustering into three patient groups of known diagnosis).  ...  We use our recently described interactive visualization tool, the Hierarchical Clustering Explorer (HCE) to systemically address the effect of different noise filters on resolution of arrays into "correct  ...  The goal was to use unsupervised hierarchical clustering to find the combination of methods that maximized the separation of the "known" biological variable, while minimizing confounding "noise".  ... 
doi:10.1109/icme.2003.1221348 dblp:conf/icmcs/SeoBZCCSH03 fatcat:khuyqe7hxjbrximbmblnff5wyi

A Comparison of Methods for Clustering 16S rRNA Sequences into OTUs

Wei Chen, Clarence K. Zhang, Yongmei Cheng, Shaowu Zhang, Hongyu Zhao, Maurizio Casiraghi
2013 PLoS ONE  
In general, hierarchical clustering methods perform better at lower dissimilarity thresholds. Our results show that sequence abundance plays an important role in OTU inference.  ...  For high-complexity data sets, hierarchical cluster methods need a more strict dissimilarity threshold to define OTUs because the commonly used dissimilarity threshold of 3% often leads to an under-estimation  ...  Alekseyenko and two anonymous reviewers for comments and discussions that improved the quality of the manuscript.  ... 
doi:10.1371/journal.pone.0070837 pmid:23967117 pmcid:PMC3742672 fatcat:3hyctlbb6nhjnk4lgb4mnlje5q

Clustering-based approaches to SAGE data mining

Haiying Wang, Huiru Zheng, Francisco Azuaje
2008 BioData Mining  
Clustering techniques have become fundamental approaches in these applications. This paper reviews relevant clustering techniques specifically designed for this type of data.  ...  It has led to several biological discoveries and biomedical applications, such as the prediction of new gene functions and the identification of biomarkers in human cancer research.  ...  include sufficient information to uniquely represent the transcript and; (2) the end-to-end concatenation of tags into long DNA molecular allows rapid, efficient sequencing analysis of multiple transcripts  ... 
doi:10.1186/1756-0381-1-5 pmid:18822151 pmcid:PMC2553774 fatcat:4ahsd5qvorhnxfqha4mh46kshy

BAR-PLUS: the Bologna Annotation Resource Plus for functional and structural annotation of protein sequences

D. Piovesan, P. Luigi Martelli, P. Fariselli, A. Zauli, I. Rossi, R. Casadio
2011 Nucleic Acids Research  
BAR + is based on a large-scale genome cross comparison and a non-hierarchical clustering procedure characterized by a metric that ensures a reliable transfer of features within clusters.  ...  When PDB templates are present within a cluster (with or without their SCOP classification), profile Hidden Markov Models (HMMs) are computed on the basis of sequence to structure alignment and are cluster-associated  ...  Hierarchical clustering categorizes sequences into a tree-structure. Examples of hierarchical clustering include SYSTERS (1), Picasso (2) and iProClass (3) .  ... 
doi:10.1093/nar/gkr292 pmid:21622657 pmcid:PMC3125743 fatcat:abdczhrn4fgwrphmutaxycsrku
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