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PyNAST: a flexible tool for aligning sequences to a template alignment

J. G. Caporaso, K. Bittinger, F. D. Bushman, T. Z. DeSantis, G. L. Andersen, R. Knight
2009 Bioinformatics  
Motivation: The Nearest Alignment Space Termination (NAST) tool is commonly used in sequence-based microbial ecology community analysis, but due to the limited portability of the original implementation  ...  Additionally because users can align to arbitrary template alignments, a feature not available via the original NAST web interface, the NAST algorithm will be readily applicable to novel tasks outside  ...  In PyNAST, the user can specify an arbitrary template alignment in a standard fasta alignment file to which candidate sequences should be aligned.  ... 
doi:10.1093/bioinformatics/btp636 pmid:19914921 pmcid:PMC2804299 fatcat:z42n3t6nkjaq3nff5hd6bubdb4

SINA: Accurate high-throughput multiple sequence alignment of ribosomal RNA genes

Elmar Pruesse, Jörg Peplies, Frank Oliver Glöckner
2012 Computer applications in the biosciences : CABIOS  
Motivation: In the analysis of homologous sequences, computation of multiple sequence alignments (MSAs) has become a bottleneck.  ...  SINA uses a combination of k-mer searching and partial order alignment (POA) to maintain very high alignment accuracy while satisfying high throughput performance demands.  ...  The authors also thank Ralf Westram for his help in interfacing SINA with ARB and his great work on ARB in general and Dr Wolfgang Ludwig for providing us with deep insights into the topics of alignment  ... 
doi:10.1093/bioinformatics/bts252 pmid:22556368 pmcid:PMC3389763 fatcat:irsdnsmxjrbchm2fvcufnhxyve

IM-TORNADO: A Tool for Comparison of 16S Reads from Paired-End Libraries

Patricio Jeraldo, Krishna Kalari, Xianfeng Chen, Jaysheel Bhavsar, Ashutosh Mangalam, Bryan White, Heidi Nelson, Jean-Pierre Kocher, Nicholas Chia, Paul Jaak Janssen
2014 PLoS ONE  
OPEN ACCESS Citation: Jeraldo P, Kalari K, Chen X, Bhavsar J, Mangalam A, et al. (2014) IM-TORNADO: A Tool for Comparison of 16S Reads from Paired-End Libraries. PLoS ONE 9(12): e114804.  ...  Illumina paired-end sequencing, which produces two separate reads for each DNA fragment, has become the platform of choice for this application.  ...  Acknowledgments The authors thank Bruce Eckloff and Á lvaro Hernández for discussion and sequencing support.  ... 
doi:10.1371/journal.pone.0114804 pmid:25506826 pmcid:PMC4266640 fatcat:l6qpijoc5vbpbfujhzauxmih5y

Microbial community dynamics of surface water in British Columbia, Canada [article]

Miguel Uyaguari, Matthew Croxen, Kirby Cronin, Zhiyao Luo, Judith Isaac-Renton, Natalie Prystajecky, Patrick Tang
2019 bioRxiv   pre-print
, as well as searching for additional microbial indicators of the health of a watershed.  ...  sequencing of the 16S rRNA gene.  ...  In PyNAST: a flexible tool for aligning sequences to a template alignment. Bioinformatics and extracellular DNA release contribute to Campylobacter jejuni biofilm formation.  ... 
doi:10.1101/719146 fatcat:jaapsd36c5ctlmubnaijhvlxpa

Cascabel: A Scalable and Versatile Amplicon Sequence Data Analysis Pipeline Delivering Reproducible and Documented Results

Alejandro Abdala Asbun, Marc A. Besseling, Sergio Balzano, Judith D. L. van Bleijswijk, Harry J. Witte, Laura Villanueva, Julia C. Engelmann
2020 Frontiers in Genetics  
We have developed Cascabel, a scalable, flexible, and easy-to-use amplicon sequence data analysis pipeline, which uses Snakemake and a combination of existing and newly developed solutions for its computational  ...  is lower than that required for metagenome sequencing.  ...  Removing singletons reduced the number of OTUs in the analyzed dataset to roughly 500, 000. To align representative sequences, we used pynast and fasttree to generate a phylogenetic tree.  ... 
doi:10.3389/fgene.2020.489357 pmid:33329686 pmcid:PMC7718033 fatcat:2kopi5d4ivac5darg5bnlj7lq4

MICCA: a complete and accurate software for taxonomic profiling of metagenomic data

Davide Albanese, Paolo Fontana, Carlotta De Filippo, Duccio Cavalieri, Claudio Donati
2015 Scientific Reports  
Bianco for useful discussions during the course of this work. This work was supported by the Autonomous Province of Trento under the project METAFOODLABS, protocol number S116/2012/537723.  ...  QIIME 2 , a recent workflow for metagenomic data analysis, integrates several tools in a single pipeline to analyse sequencing data including also the possibility to display the results in a graphical  ...  1 , a pipeline for targeted metagenomic data incorporating several tools for sequence filtering, OTUs definition and estimate of ecological parameters.  ... 
doi:10.1038/srep09743 pmid:25988396 pmcid:PMC4649890 fatcat:3bwd4wgnrjamvnqb32dd7ujbry

HmmUFOtu: An HMM and phylogenetic placement based ultra-fast taxonomic assignment and OTU picking tool for microbiome amplicon sequencing studies

Qi Zheng, Casey Bartow-McKenney, Jacquelyn S. Meisel, Elizabeth A. Grice
2018 Genome Biology  
Here, we present HmmUFOtu, a novel tool for processing microbiome amplicon sequencing data, which performs rapid per-read phylogenetic placement, followed by phylogenetically informed clustering into OTUs  ...  Typical analysis pipelines group sequences into operational taxonomic units (OTUs) to infer taxonomic and phylogenetic relationships.  ...  Acknowledgements We thank Kyle Bittinger for his invaluable input on improving HmmUFOtu; we also thank Joseph Horwinski for constructing and sequencing the mock community libraries used in our previous  ... 
doi:10.1186/s13059-018-1450-0 pmid:29950165 pmcid:PMC6020470 fatcat:uto7cbvcnrgi5ka3g2qj4yjxz4

Diazotroph Community Characterization via a High-Throughput nifH Amplicon Sequencing and Analysis Pipeline

John Christian Gaby, Lavanya Rishishwar, Lina C. Valderrama-Aguirre, Stefan J. Green, Augusto Valderrama-Aguirre, I. King Jordan, Joel E. Kostka, M. Julia Pettinari
2017 Applied and Environmental Microbiology  
In this study, a flexible sequencing/analysis pipeline, named TaxADivA, was developed for nifH amplicons produced by Illumina paired-end sequencing, and it enables an inference of taxonomy, performs clustering  ...  To improve nifH sequence analysis, we developed a computational pipeline which infers taxonomy and optionally filters out paralog sequences.  ...  Konstantinidis for use of their Illumina MiSeq machine, and Jack Gilbert for helpful discussion on how to improve the pipeline.  ... 
doi:10.1128/aem.01512-17 pmid:29180374 pmcid:PMC5795091 fatcat:ho6kv7c7fnga5jyu6mvhashc7a

Modelling Computational Resources for Next Generation Sequencing Bioinformatics Analysis of 16S rRNA Samples [article]

Matthew J. Wade and Thomas P. Curtis and Russell J. Davenport
2015 arXiv   pre-print
The models were able to accurately predict clock time for denoising sequences from a naturally assembled community dataset, but not an artificial community.  ...  A novel method for predicting time to completion for a popular bioinformatics software (QIIME), was developed using key variables characteristic of the input data assumed to impact processing time.  ...  Alignment was performed using the PyNAST method and pairwise clustering with uclust [7] against a Greengenes database template.  ... 
arXiv:1503.02974v1 fatcat:gsavmjldgfezbnwyqtxfxq4p6q

The Effects of Freezing on Faecal Microbiota as Determined Using MiSeq Sequencing and Culture-Based Investigations

Fiona Fouhy, Jennifer Deane, Mary C. Rea, Órla O'Sullivan, R. Paul Ross, Grace O'Callaghan, Barry J. Plant, Catherine Stanton, Josef Neu
2015 PLoS ONE  
Type of publication Article ( peer-reviewed) Link to publisher's version http://dx.doi.org/10.1371/journal.pone.0119355 Access to the full text of the published version may require a subscription.  ...  Samples were separated into fresh (DNA extracted immediately), snap frozen on dry ice and frozen for 7 days at -80°C prior to DNA extraction or samples frozen at -80°C for 7 days before DNA extraction.  ...  Acknowledgments The authors wish to thank Dr. Fiona Crispie and Ms. Vicki Murray for their technical assistance with MiSeq sequencing.  ... 
doi:10.1371/journal.pone.0119355 pmid:25748176 pmcid:PMC4352061 fatcat:62st7bka7jhitovrdkjunfbbcu

A Phylogenomic View of Ecological Specialization in the Lachnospiraceae, a Family of Digestive Tract-Associated Bacteria

Conor J. Meehan, Robert G. Beiko
2014 Genome Biology and Evolution  
Members of this family have been linked to obesity and protection from colon cancer in humans, mainly due to the association of this group with the production of butyric acid, a substance that is important  ...  for both microbial and host epithelial cell growth.  ...  Petra Louis for supplying the BCoAT database sequences and for discussion of butyrate production. We also thank Morgan Langille, Eva 465 Boon, Katherine Dunn and W.  ... 
doi:10.1093/gbe/evu050 pmid:24625961 pmcid:PMC3971600 fatcat:h35s63ncqfenbpfnpkfmo3rwre

Microbial communities associated with the degradation of oak wood in the Blanes submarine canyon and its adjacent open slope (NW Mediterranean)

S.K. Fagervold, S. Bessette, C. Romano, D. Martin, M. Plyuscheva, N. Le Bris, P.E. Galand
2013 Progress in Oceanography  
Furthermore, an in depth taxonomic analysis revealed that Alphaproteobacteria was the dominant microbial taxa, with the 15 Roseobacter clade seeming to have a specialized role in the degradation of oak  ...  Sunken wood creates a unique ecosystem in the deep sea, which base, i.e. the microbial communities directly degrading this wood, remains poorly studied.  ...  We would like to thank M. T. Suzuki for his help with installing and updating Qiime and Mothur on local computer servers and we would like to thank F. Pititto for preparing the map.  ... 
doi:10.1016/j.pocean.2013.07.012 fatcat:ktu754tpfrazrfg325joj45pqm

Bacterial community profiles andVibrio parahaemolyticusabundance in individual oysters and their association with estuarine ecology [article]

Ashley L. Marcinkiewicz, Brian M. Schuster, Stephen H. Jones, Vaughn S. Cooper, Cheryl A. Whistler
2017 bioRxiv   pre-print
of sequencing may reveal microbiome members that could impactV. parahaemolyticusabundance.  ...  This study, which to our knowledge is the first of its kind to evaluate associations ofV. parahaemolyticusabundance with members of individual oyster microbiomes, implies that sufficient sampling and depth  ...  PyNAST: A 624 flexible tool for aligning sequences to a template alignment. Bioinformatics. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool.  ... 
doi:10.1101/156851 fatcat:lruhtut2hbfmhav5qmudcathuy

Advancing Our Understanding of the Human Microbiome Using QIIME [chapter]

José A. Navas-Molina, Juan M. Peralta-Sánchez, Antonio González, Paul J. McMurdie, Yoshiki Vázquez-Baeza, Zhenjiang Xu, Luke K. Ursell, Christian Lauber, Hongwei Zhou, Se Jin Song, James Huntley, Gail L. Ackermann (+4 others)
2013 Methods in Enzymology  
QIIME (Quantitative Insights Into Microbial Ecology) is an open-source bioinformatics software package designed for microbial community analysis based on DNA sequence data, which provides a single analysis  ...  We present examples of some of the types of analyses that are enabled by QIIME and discuss how other tools, such as phyloseq and R, can be applied to expand upon these analyses.  ...  We also acknowledge Manuel Lladser for helping collect the dataset and allowing us to use it, and the IQBio IGERT grant for funding data collection.  ... 
doi:10.1016/b978-0-12-407863-5.00019-8 pmid:24060131 pmcid:PMC4517945 fatcat:w6yem3w3szdwteqmqe7t6z7ikq

Diet-induced changes to host gut microbiota are linked to foraging innovation in a wild bird [article]

Gabrielle Davidson, Niamh Wiley, Amy C Cooke, Crystal N Johnson, Fiona Fouhy, Michael S Reichert, Ivan de la Hera, Jodie M.S. Crane, Ipek G Kulahci, R Paul Ross, Catherine Stanton, John L Quinn
2019 bioRxiv   pre-print
This is the first demonstration of an association between innovative problem solving and the gut microbiome in a wild animal.  ...  Individuals were less likely to problem solve after being given the insect diet, and performance was positively associated with microbiome diversity.  ...  OTUs were aligned using PyNAST (PyNAST: python nearest alignment space termination; a 179 flexible tool for aligning sequences to a template alignment) and taxonomy was assigned using 180 BLAST against  ... 
doi:10.1101/827741 fatcat:ktnflcpzpfgkxev77ateq3c6zy
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