scholarly journals LINbase: a web server for genome-based identification of prokaryotes as members of crowdsourced taxa

2020 ◽  
Vol 48 (W1) ◽  
pp. W529-W537 ◽  
Author(s):  
Long Tian ◽  
Chengjie Huang ◽  
Reza Mazloom ◽  
Lenwood S Heath ◽  
Boris A Vinatzer
Keyword(s):  
New Species ◽  
High Throughput ◽  
Web Server ◽  
Short Description ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
Genome Phylogeny ◽  
High Throughput Dna Sequencing ◽  
The Individual ◽  
Prokaryotic Taxonomy

Abstract High throughput DNA sequencing in combination with efficient algorithms could provide the basis for a highly resolved, genome phylogeny-based and digital prokaryotic taxonomy. However, current taxonomic practice continues to rely on cumbersome journal publications for the description of new species, which still constitute the smallest taxonomic units. In response, we introduce LINbase, a web server that allows users to genomically circumscribe any group of prokaryotes with measurable DNA similarity and that uses the individual isolate as smallest unit. Since LINbase leverages the concept of Life Identification Numbers (LINs), which are codes assigned to individual genomes based on reciprocal average nucleotide identity, we refer to groups circumscribed in LINbase as LINgroups. Users can associate with each LINgroup a name, a short description, and a URL to a peer-reviewed publication. As soon as a LINgroup is circumscribed, any user can immediately identify query genomes as members and submit comments about the LINgroup. Most genomes currently in LINbase were imported from GenBank, but users can upload their own genome sequences as well. In conclusion, LINbase combines the resolution of LINs with the power of crowdsourcing in support of a highly resolved, genome phylogeny-based digital taxonomy. LINbase is available at http://www.LINbase.org.

scholarly journals LINbase: A Web service for genome-based identification of microbes as members of crowdsourced taxa

2019 ◽  
Author(s):  
Long Tian ◽  
Chengjie Huang ◽  
Lenwood S. Heath ◽  
Boris A. Vinatzer
Keyword(s):  
New Species ◽  
Dna Sequencing ◽  
Web Service ◽  
Scientific Community ◽  
Disease Outbreaks ◽  
Short Description ◽  
Third Generation ◽  
Genome Sequences ◽  
Sequencing Technologies ◽  
The Web

AbstractThe development of next generation and third generation DNA sequencing technologies in combination with new efficient algorithms allows scientists to economically, quickly, and precisely identify microbes at all taxonomic levels and even attribute pathogen isolates to specific disease outbreaks. However, current taxonomic practice has not kept up with the sequencing revolution and continues to rely on cumbersome journal publications to describe new species. Here we introduce a Web service that allows any user to genomically circumscribe any monophyletic group of bacteria as a taxon and associate with each taxon a name and short description. Any other user can immediately identify their unknown microbe as a member of any of these crowdsourced taxa using gene or genome sequences. The Web service is called LINbase. It leverages the previously described concept of Life Identification Numbers (LINs), which are codes assigned to individual organisms based on genome similarity. Most genomes currently in LINbase were imported from GenBank, but users have the option to upload their own genome sequences as well. Importantly, LINbase allows users to share the precise identity of their sequenced genomes without sharing the actual genome sequences, making not yet published or private genome sequences discoverable by the scientific community stimulating collaboration between academia and industry. LINbase is available at http://www.LINbase.org.

scholarly journals AGP: A Multimethods Web Server for Alignment-Free Genome Phylogeny

2013 ◽  
Vol 30 (5) ◽  
pp. 1032-1037 ◽  
Author(s):  
Jinkui Cheng ◽  
Fuliang Cao ◽  
Zhihua Liu
Keyword(s):  
Web Server ◽  
Data Sets ◽  
Whole Genome ◽  
Alignment Method ◽  
Genome Sequences ◽  
Alignment Free ◽  
Tree Construction ◽  
Comparison Functions ◽  
Genome Phylogeny ◽  
User Friendly

Abstract Phylogenetic analysis based on alignment method meets huge challenges when dealing with whole-genome sequences, for example, recombination, shuffling, and rearrangement of sequences. Thus, various alignment-free methods for phylogeny construction have been proposed. However, most of these methods have not been implemented as tools or web servers. Researchers cannot use these methods easily with their data sets. To facilitate the usage of various alignment-free methods, we implemented most of the popular alignment-free methods and constructed a user-friendly web server for alignment-free genome phylogeny (AGP). AGP integrated the phylogenetic tree construction, visualization, and comparison functions together. Both AGP and all source code of the methods are available at http://www.herbbol.org:8000/agp (last accessed February 26, 2013). AGP will facilitate research in the field of whole-genome phylogeny and comparison.

scholarly journals Chemiluminiscence sensor for high-throughput DNA sequencing

2009 ◽  
Vol 1 (1) ◽  
pp. 1091-1094
Author(s):  
A R A Rahman ◽  
Shihui Foo ◽  
Sanket Goel
Keyword(s):  
Dna Sequencing ◽  
High Throughput ◽  
High Throughput Dna Sequencing

scholarly journals Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 16 ◽  
Author(s):  
Michael P Mullen ◽  
Christopher J Creevey ◽  
Donagh P Berry ◽  
Matt S McCabe ◽  
David A Magee ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Allele Frequency ◽  
High Throughput ◽  
Frequency Estimation ◽  
Allele Frequency Estimation ◽  
Polymorphism Discovery ◽  
Pooled Dna ◽  
High Throughput Dna Sequencing

Application of high-throughput DNA sequencing to score population-specific variants for rare disorders

2019 ◽  
Vol 305 ◽  
pp. S25
Author(s):  
M.C. Ergoren ◽  
E. Manara ◽  
S. Paolacci ◽  
S.G. Temel ◽  
G. Mocan ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
High Throughput ◽  
Rare Disorders ◽  
High Throughput Dna Sequencing

scholarly journals A problematic cnidarian (Cambroctoconus; Octocorallia?) from the Cambrian (Series 2–3) of Laurentia

2017 ◽  
Vol 91 (5) ◽  
pp. 871-882 ◽  
Author(s):  
John S. Peel
Keyword(s):  
New Species ◽  
Fossil Record ◽  
First Record ◽  
Soft Corals ◽  
Pore System ◽  
General Development ◽  
Stage 4 ◽  
Basal Clade ◽  
The Individual ◽  
North Greenland

AbstractThe problematic calcified cnidarian Cambroctoconus is described from the Henson Gletscher Formation (Cambrian Series 2, Stage 4–Series 3, Stage 5) of North Greenland, representing the first record from Laurentia of a genus otherwise recently described from China, Kyrgyzstan, and Korea. Internal molds produced by penetrative phosphatization mirror the pervasive pore system of the calice walls and septa. The pore system is compared to the network of gastrodermal solenia that distributes nutrients between polyps and surrounding stolon tissues in present day octocorals. In conjunction with the octagonal form of the individual coralla and eight-fold symmetry of septa, the pore system promotes assignment of Cambroctoconus to the Octocorallia, a basal clade in cnidarian phylogeny. Octocorals (‘soft corals’) are diverse in present day seas, but have a poor fossil record despite the general development of distinctive calcareous spicules. New taxa: Order Cambroctoconida new; Cambroctoconus koori new species.

scholarly journals Omics in a Digital World: The Role of Bioinformatics in Providing New Insights Into Human Aging

2021 ◽  
Vol 12 ◽  
Author(s):  
Serena Dato ◽  
Paolina Crocco ◽  
Nicola Rambaldi Migliore ◽  
Francesco Lescai
Keyword(s):  
High Throughput ◽  
Aging Process ◽  
Single Cell Analysis ◽  
Physiological Age ◽  
Data Types ◽  
Aging Research ◽  
Digital World ◽  
Age Related ◽  
Critical Issues ◽  
The Individual

BackgroundAging is a complex phenotype influenced by a combination of genetic and environmental factors. Although many studies addressed its cellular and physiological age-related changes, the molecular causes of aging remain undetermined. Considering the biological complexity and heterogeneity of the aging process, it is now clear that full understanding of mechanisms underlying aging can only be achieved through the integration of different data types and sources, and with new computational methods capable to achieve such integration.Recent AdvancesIn this review, we show that an omics vision of the age-dependent changes occurring as the individual ages can provide researchers with new opportunities to understand the mechanisms of aging. Combining results from single-cell analysis with systems biology tools would allow building interaction networks and investigate how these networks are perturbed during aging and disease. The development of high-throughput technologies such as next-generation sequencing, proteomics, metabolomics, able to investigate different biological markers and to monitor them simultaneously during the aging process with high accuracy and specificity, represents a unique opportunity offered to biogerontologists today.Critical IssuesAlthough the capacity to produce big data drastically increased over the years, integration, interpretation and sharing of high-throughput data remain major challenges. In this paper we present a survey of the emerging omics approaches in aging research and provide a large collection of datasets and databases as a useful resource for the scientific community to identify causes of aging. We discuss their peculiarities, emphasizing the need for the development of methods focused on the integration of different data types.Future DirectionsWe critically review the contribution of bioinformatics into the omics of aging research, and we propose a few recommendations to boost collaborations and produce new insights. We believe that significant advancements can be achieved by following major developments in bioinformatics, investing in diversity, data sharing and community-driven portable bioinformatics methods. We also argue in favor of more engagement and participation, and we highlight the benefits of new collaborations along these lines. This review aims at being a useful resource for many researchers in the field, and a call for new partnerships in aging research.

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