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 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.

Gifts from the Web: Service Learning

2005 ◽  
Vol 8 (1) ◽  
pp. 16-18
Author(s):  
Howard F. Wilson
Keyword(s):  
Service Learning ◽  
Web Service ◽  
The Web

New species list of plants and lichens of Russia for Turboveg for Windows

2020 ◽  
pp. 151-156
Author(s):  
A. P. Korablev ◽  
N. S. Liksakova ◽  
D. M. Mirin ◽  
D. G. Oreshkin ◽  
P. G. Efimov
Keyword(s):  
New Species ◽  
Vascular Plants ◽  
Russian Literature ◽  
Web Page ◽  
Species List ◽  
Internet Resources ◽  
The World ◽  
A New Species ◽  
The Web

A new species list of plants and lichens of Russia and neighboring countries has been developed for Turboveg for Windows, the program, intended for storage and management of phytosociological data (relevés), is widely used all around the world (Hennekens, Schaminée, 2001; Hennekens, 2015). The species list is built upon the database of the Russian website Plantarium (Plantarium…: [site]), which contains a species atlas and illustrated an online Handbook of plants and lichens. The nomenclature used on Plantarium was originally based on the following issues: vascular plants — S. K. Cherepanov (1995) with additions; mosses — «Flora of mosses of Russia» (Proect...: [site]); liverworts and hornworts — A. D. Potemkin and E. V. Sofronova (2009); lichens — «Spisok…» G. P. Urbanavichyus ed. (2010); other sources (Plantarium...: [site]). The new species list, currently the most comprehensive in Turboveg format for Russia, has 89 501 entries, including 4627 genus taxa compare to the old one with 32 020 entries (taxa) and only 253 synonyms. There are 84 805 species and subspecies taxa in the list, 37 760 (44.7 %) of which are accepted, while the others are synonyms. Their distribution by groups of organisms and divisions are shown in Table. A large number of synonyms in the new list and its adaptation to work with the Russian literature will greatly facilitate the entry of old relevé data. The ways of making new list, its structure as well as the possibilities of checking taxonomic lists on Internet resources are considered. The files of the species list for Turboveg 2 and Turboveg 3, the technique of associating existing databases with a new species list (in Russian) are available on the web page https://www.binran.ru/resursy/informatsionnyye-resursy/tekuschie-proekty/species_list_russia/.

Web Services Architecture Model to Support Distributed Systems

2019 ◽  
Vol 54 (6) ◽  
Author(s):  
Sawsan Ali Hamid ◽  
Rana Alauldeen Abdalrahman ◽  
Inam Abdullah Lafta ◽  
Israa Al Barazanchi
Keyword(s):  
Web Services ◽  
Web Service ◽  
Distributed System ◽  
Modern Technology ◽  
Service Description ◽  
Architecture Model ◽  
Software Applications ◽  
Evolving Model ◽  
The Web

Recently, web services have presented a new and evolving model for constructing the distributed system. The meteoric growth of the Web over the last few years proves the efficacy of using simple protocols over the Internet as the basis for a large number of web services and applications. Web service is a modern technology of web, which can be defined as software applications with a programmatic interface based on Internet protocol. Web services became common in the applications of the web by the help of Universal, Description, Discovery and Integration; Web Service Description Language and Simple Object Access Protocol. The architecture of web services refers to a collection of conceptual components in which common sets of standard can be defined among interoperating components. Nevertheless, the existing Web service's architecture is not impervious to some challenges, such as security problems, and the quality of services. Against this backdrop, the present study will provide an overview of these issues. Therefore, it aims to propose web services architecture model to support distributed system in terms of application and issues.

scholarly journals Apollo: a sequencing-technology-independent, scalable and accurate assembly polishing algorithm

2020 ◽  
Vol 36 (12) ◽  
pp. 3669-3679 ◽  
Author(s):  
Can Firtina ◽  
Jeremie S Kim ◽  
Mohammed Alser ◽  
Damla Senol Cali ◽  
A Ercument Cicek ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Supplementary Information ◽  
Third Generation ◽  
Sequencing Technology ◽  
Base Pairs ◽  
Sequencing Technologies ◽  
Third Generation Sequencing ◽  
Long Reads ◽  
Generation Sequencing ◽  
Large Genomes

Abstract Motivation Third-generation sequencing technologies can sequence long reads that contain as many as 2 million base pairs. These long reads are used to construct an assembly (i.e. the subject’s genome), which is further used in downstream genome analysis. Unfortunately, third-generation sequencing technologies have high sequencing error rates and a large proportion of base pairs in these long reads is incorrectly identified. These errors propagate to the assembly and affect the accuracy of genome analysis. Assembly polishing algorithms minimize such error propagation by polishing or fixing errors in the assembly by using information from alignments between reads and the assembly (i.e. read-to-assembly alignment information). However, current assembly polishing algorithms can only polish an assembly using reads from either a certain sequencing technology or a small assembly. Such technology-dependency and assembly-size dependency require researchers to (i) run multiple polishing algorithms and (ii) use small chunks of a large genome to use all available readsets and polish large genomes, respectively. Results We introduce Apollo, a universal assembly polishing algorithm that scales well to polish an assembly of any size (i.e. both large and small genomes) using reads from all sequencing technologies (i.e. second- and third-generation). Our goal is to provide a single algorithm that uses read sets from all available sequencing technologies to improve the accuracy of assembly polishing and that can polish large genomes. Apollo (i) models an assembly as a profile hidden Markov model (pHMM), (ii) uses read-to-assembly alignment to train the pHMM with the Forward–Backward algorithm and (iii) decodes the trained model with the Viterbi algorithm to produce a polished assembly. Our experiments with real readsets demonstrate that Apollo is the only algorithm that (i) uses reads from any sequencing technology within a single run and (ii) scales well to polish large assemblies without splitting the assembly into multiple parts. Availability and implementation Source code is available at https://github.com/CMU-SAFARI/Apollo. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals From Genetics to Genomics of Epilepsy

2012 ◽  
Vol 2012 ◽  
pp. 1-18 ◽  
Author(s):  
Silvio Garofalo ◽  
Marisa Cornacchione ◽  
Alfonso Di Costanzo
Keyword(s):  
Dna Sequencing ◽  
Dna Microarrays ◽  
Molecular Cytogenetics ◽  
Entire Genome ◽  
Sequencing Technologies ◽  
Genomic Approach ◽  
Molecular Karyotype ◽  
High Throughput Dna Sequencing ◽  
Laboratory Technology ◽  
Near Future

The introduction of DNA microarrays and DNA sequencing technologies in medical genetics and diagnostics has been a challenge that has significantly transformed medical practice and patient management. Because of the great advancements in molecular genetics and the development of simple laboratory technology to identify the mutations in the causative genes, also the diagnostic approach to epilepsy has significantly changed. However, the clinical use of molecular cytogenetics and high-throughput DNA sequencing technologies, which are able to test an entire genome for genetic variants that are associated with the disease, is preparing a further revolution in the near future. Molecular Karyotype and Next-Generation Sequencing have the potential to identify causative genes or loci also in sporadic or non-familial epilepsy cases and may well represent the transition from a genetic to a genomic approach to epilepsy.

Test genetici e consenso informato

2012 ◽  
pp. 68-95
Author(s):  
Marco Seri ◽  
Claudio Graziano ◽  
Daniela Turchetti ◽  
Juri Monducci
Keyword(s):  
Dna Sequencing ◽  
Human Genetics ◽  
Ethical Issues ◽  
Clinical Care ◽  
Genomic Medicine ◽  
Genome Project ◽  
Ethical Challenges ◽  
Sequencing Technologies ◽  
The Human Genome Project

The pace of discovery in the field of human genetics has increased exponentially in the last 30 years. We have witnessed the completion of the Human Genome Project, the identification of hundreds of disease-causing genes, and the dawn of genomic medicine (clinical care based on genomic information). Reduction of DNA sequencing costs, thanks to the so-called "next generation sequencing" technologies, is driving a shift towards the era of "personal genomes", but scientific as well as ethical challenges ahead are countless. We provide an overview on the classification of genetic tests, on informed consent procedures in the context of genetic counseling, and on specific ethical issues raised by the implementation of new DNA sequencing technologies.

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