scholarly journals Geno2proteo, a Tool for Batch Retrieval of DNA and Protein Sequences from Any Genomic or Protein Regions

2019 ◽  
Vol 16 (3) ◽  
Author(s):  
Yaoyong Li ◽  
Elisa Aguilar-Martinez ◽  
Andrew D. Sharrocks
Keyword(s):  
Web Service ◽  
Sequence Data ◽  
Protein Sequences ◽  
R Package ◽  
Amino Acid Sequences ◽  
Important Task ◽  
Web Interface ◽  
Web Page ◽  
Dna Sequence Data ◽  
The Web

AbstractThe interconversion of sequences that constitute the genome and the proteome is becoming increasingly important due to the generation of large amounts of DNA sequence data. Following mapping of DNA segments to the genome, one fundamentally important task is to find the amino acid sequences which are coded within a list of genomic sections. Conversely, given a series of protein segments, an important task is to find the genomic loci which code for a list of protein regions. To perform these tasks on a region by region basis is extremely laborious when a large number of regions are being studied. We have therefore implemented an R package geno2proteo which performs the two mapping tasks and subsequent sequence retrieval in a batch fashion. In order to make the tool more accessible to users, we have created a web interface of the R package which allows the users to perform the mapping tasks by going to the web page http://sharrocksresources.manchester.ac.uk/tofigaps and using the web service.

scholarly journals Techniques for the verification of minimal phylogenetic trees illustrated with ten mammalian haemoglobin sequences

1980 ◽  
Vol 187 (1) ◽  
pp. 65-74 ◽  
Author(s):  
D Penny ◽  
M D Hendy ◽  
L R Foulds
Keyword(s):  
Amino Acid ◽  
Phylogenetic Tree ◽  
Protein Sequence ◽  
Phylogenetic Trees ◽  
Sequence Data ◽  
Protein Sequences ◽  
Nucleotide Sequences ◽  
Amino Acid Sequences ◽  
Minimal Tree ◽  
Protein Sequence Data

We have recently reported a method to identify the shortest possible phylogenetic tree for a set of protein sequences [Foulds Hendy & Penny (1979) J. Mol. Evol. 13. 127–150; Foulds, Penny & Hendy (1979) J. Mol. Evol. 13, 151–166]. The present paper discusses issues that arise during the construction of minimal phylogenetic trees from protein-sequence data. The conversion of the data from amino acid sequences into nucleotide sequences is shown to be advantageous. A new variation of a method for constructing a minimal tree is presented. Our previous methods have involved first constructing a tree and then either proving that it is minimal or transforming it into a minimal tree. The approach presented in the present paper progressively builds up a tree, taxon by taxon. We illustrate this approach by using it to construct a minimal tree for ten mammalian haemoglobin alpha-chain sequences. Finally we define a measure of the complexity of the data and illustrate a method to derive a directed phylogenetic tree from the minimal tree.

scholarly journals The MG-RAST API explorer: an on-ramp for RESTful query composition

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Tobias Paczian ◽  
William L. Trimble ◽  
Wolfgang Gerlach ◽  
Travis Harrison ◽  
Andreas Wilke ◽  
...  
Keyword(s):  
Sequence Data ◽  
Web Interface ◽  
Function Data ◽  
Barrier To Entry ◽  
And Function ◽  
First Time ◽  
The Web

Abstract Background The MG-RAST API provides search capabilities and delivers organism and function data as well as raw or annotated sequence data via the web interface and its RESTful API. For casual users, however, RESTful APIs are hard to learn and work with. Results We created the graphical MG-RAST API explorer to help researchers more easily build and export API queries; understand the data abstractions and indices available in MG-RAST; and use the results presented in-browser for exploration, development, and debugging. Conclusions The API explorer lowers the barrier to entry for occasional or first-time MG-RAST API users.

scholarly journals Phylogeny of Anophelinae using mitochondrial protein coding genes

2017 ◽  
Vol 4 (11) ◽  
pp. 170758 ◽  
Author(s):  
Peter G. Foster ◽  
Tatiane Marques Porangaba de Oliveira ◽  
Eduardo S. Bergo ◽  
Jan E. Conn ◽  
Denise Cristina Sant’Ana ◽  
...  
Keyword(s):  
Sequence Data ◽  
Mitochondrial Protein ◽  
Amino Acid Sequences ◽  
Protein Coding ◽  
Natural Classification ◽  
Marginalized Communities ◽  
Dna Sequence Data ◽  
Protein Coding Genes ◽  
Genus Level ◽  
Vector Borne

Malaria is a vector-borne disease that is a great burden on the poorest and most marginalized communities of the tropical and subtropical world. Approximately 41 species of Anopheline mosquitoes can effectively spread species of Plasmodium parasites that cause human malaria. Proposing a natural classification for the subfamily Anophelinae has been a continuous effort, addressed using both morphology and DNA sequence data. The monophyly of the genus Anopheles , and phylogenetic placement of the genus Bironella , subgenera Kerteszia , Lophopodomyia and Stethomyia within the subfamily Anophelinae, remain in question. To understand the classification of Anophelinae, we inferred the phylogeny of all three genera ( Anopheles , Bironella , Chagasia ) and major subgenera by analysing the amino acid sequences of the 13 protein coding genes of 150 newly sequenced mitochondrial genomes of Anophelinae and 18 newly sequenced Culex species as outgroup taxa, supplemented with 23 mitogenomes from GenBank. Our analyses generally place genus Bironella within the genus Anopheles , which implies that the latter as it is currently defined is not monophyletic. With some inconsistencies, Bironella was placed within the major clade that includes Anopheles , Cellia , Kerteszia , Lophopodomyia , Nyssorhynchus and Stethomyia , which were found to be monophyletic groups within Anophelinae. Our findings provided robust evidence for elevating the monophyletic groupings Kerteszia , Lophopodomyia , Nyssorhynchus and Stethomyia to genus level; genus Anopheles to include subgenera Anopheles , Baimaia , Cellia and Christya ; Anopheles parvus to be placed into a new genus; Nyssorhynchus to be elevated to genus level; the genus Nyssorhynchus to include subgenera Myzorhynchella and Nyssorhynchus ; Anopheles atacamensis and Anopheles pictipennis to be transferred from subgenus Nyssorhynchus to subgenus Myzorhynchella ; and subgenus Nyssorhynchus to encompass the remaining species of Argyritarsis and Albimanus Sections.

scholarly journals Online Database for Retrieval Information about Prebiotics and Their Activity

2020 ◽  
Vol 10 (9) ◽  
pp. 3328
Author(s):  
Elena Guseva ◽  
Boris Karetkin ◽  
Diana Batyrgazieva ◽  
Natalia Menshutina ◽  
Victor Panfilov
Keyword(s):  
Chemical Nature ◽  
Scientific Information ◽  
Scientific Development ◽  
The Internet ◽  
Online Database ◽  
Web Interface ◽  
Web Page ◽  
Practical Development ◽  
On Line ◽  
The Web

The number of studies aimed at proving the prebiotic properties of certain substances or compositions has been actively increasing, which has led to a large accumulation of scientific information that is fragmented and not systematized. Moreover, a number of criteria have been applied in these studies. The lack of an accessible and convenient information space to compare the obtained results seems to hold back not only scientific development, but also practical development in this field. A database called the «On-line Database of Researches on Activity of Prebiotics» (ODRAP) is presented in this article, which contains information about both prebiotics and some probiotics, that were used in these researches. Currently, ODRAP collects 25 bacteria genera or their combinations, 59 bacteria species, 140 prebiotic substances, 61 prebiotic production companies, 2 methods of fermentation, and 271 analyzed articles from 2001 till 2019. To facilitate access to the database, a special Web-interface was created, which allows any user who opens the Web-page to obtain information about the features and activities of prebiotics, as well as to sort the data by species and genus of bacteria applied in tests, the chemical nature or source of prebiotics, and other parameters. The convenience of the Web-interface is that it allows access to the database, regardless of the user platform and from anywhere, via the Internet.

scholarly journals Penerapan Data JSON Untuk Mendukung Pengembangan Aplikasi Pada Perguruan Tinggi Dengan Teknik Restfull Dan Web Service

2017 ◽  
Vol 2 (1) ◽  
pp. 26-36
Author(s):  
Ary Budi Warsito ◽  
Ajeng Ananda ◽  
Dian Triyanjaya
Keyword(s):  
Information System ◽  
Data Collection ◽  
Web Service ◽  
Data Retrieval ◽  
Web Page ◽  
Large Bandwidth ◽  
Data Collection Process ◽  
Hypertext Transfer Protocol ◽  
The Web ◽  
Transfer Protocol

Data  adalah  salah  satu  komponen  penting  dalam  sebuah  aplikasi.  Di  perlukan  sebuah  database untuk  menyimpan  data  dalam jumlah  besar  sebagai  media  pendistribusian  data  dari  server  ke client.  Banyak  nya  aplikasi  pada  sebuah  perguruan  tinggi  membutuhkan  bandwidth  yang  besar untuk  keperluan  pengambilan  data  untuk  di  sajikan  sebagai  sistem  informasi  yang  sangat berguna  untuk  berbagai  kepentingan.  Web  Service  sangat  berperan  penting  pada  kasus  ini dimana,  client  yang  seharusnya  mengakses  melalui  jalur  yang  berbeda  ke  database  akan  di alihkan  ke  dalam  web service dalam proses pengambilan data untuk meringankan kerja database yang harus  berulang  ulang  melayani  permintaan  dari  client.  Arsitektur  REST,  yang  pada dasarnya di  oprasikan  melalui  HTTP (Hypertext Transfer Protocol), yang mengacu pada proses pembacaan  halaman  web  tertentu  yang  berisi  sebuah  file  JSON.  File  inilah  yang  menguraikan dan  memuat  konten  yang  hendak  disajikan  kepada  konsumen.  Setelah  melalui  sebuah  proses definisi  tertentu, konsumen  akan bisa mengakses antarmuka aplikasi yang  tersedia. Kata Kunci :  Database, Web Service, permintaan  Data is one of the important components in an application. In need of a database to store large amounts of data as a medium for the distribution of data from the server to the client. Many of its application on a college requires a large bandwidth for data retrieval purposes toserved as an information system that is very useful for various purposes. Web Service is very important in this case where, clients should access through different pathways to the database will switch to the web service in the data collection process to alleviate the database that should be repeated requests  from  the  client.  REST  architecture,  which  is  basically  in  oprasik an  via  HTTP (Hypertext Transfer Protocol), which refers to the process of reading a specific web page that contains a JSON file. It is this file that describes and includes the content to be presented to consumers.  After  going  through a process of certain definitions, consumers will be able to access the application interface is available. Keywords: Database, Web Service, request  

scholarly journals Nicosia and Palmanova: Images of the city in the digital environment

2016 ◽  
Vol 5 (2) ◽  
Author(s):  
Gokce Kececi ◽  
Gamze Anıl
Keyword(s):  
Cultural Heritage ◽  
Life Forms ◽  
Web Pages ◽  
Digital Environment ◽  
Web Interface ◽  
Web Page ◽  
Social Differences ◽  
The City ◽  
Day By Day ◽  
The Web

As it is known, the existence of star-shaped cities went back to 16th century. Although these cities include different life forms because of the reason why they were established, at the same time, they share structural similarities. There are nine star-shaped cities in the world and can be found in Italy, Cyprus, Japan, Holland, Canada, Vietnam, Finland and Russia. Because the same architect designed Nicosia and Palmanova in Italy, the study will begin with a broader view on star-shaped cities and compare both. Although the walls were designed for defensive purposes, today, they are protected as a cultural heritage and this is significant for tourism. In this context, this study will analyse the web interface and how both Palmanova and Nicosia use the web, in terms of content, visual aspects, and how these are being used. As the number of users for web pages and blogs are increasing day by day, The reflection of social differences has been researched by examining the Lefkosa-Palmanova examples. Keywords: star-shaped, city cultural heritage, web page, blog 

scholarly journals Tankmate Design for Settings Filter, Temperature, and Light on Aquascape

2019 ◽  
Vol 54 (5) ◽  
Author(s):  
Tata Sutabri ◽  
Yohanes Bowo Widodo ◽  
Sondang Sibuea ◽  
Ismi Rajiani ◽  
Yaziz Hasan
Keyword(s):  
Control System ◽  
Web Service ◽  
Online Control ◽  
Remote Access ◽  
Water Filtration ◽  
Communication Line ◽  
Web Interface ◽  
Front End ◽  
Spiral Model ◽  
The Web

The success of aquascape maintenance lies in certain critical factors, including temperatures, lights and water filtration, which should be constantly monitored; but at some point, these keys are not well monitored, causing correctional action being taken too late and creating damage. Using an online control system as an IoT device can assist in control and automation functions, while an online feature provides monitoring, remote access, and remote override as other benefits that would help maintain an aquascape. This research’s subject involves designing an IoT device as an online control system that would automatically control temperatures, lights and water filtration using an Arduino-compatible board based on an ATMega328/P microcontroller connected to web services and a web portal for a monitoring and management interface. This control system uses Wi-Fi as a communication line with the web service. API is a bridge from the control system and the web service, and the portal’s front end and back end are custom-built using PHP and MySQL. The overall process was developed using a combination of the spiral model and prototyping paradigm modelling. The result is a fully working prototype of an online control system complete with a web interface, which helps aquascapers maintain their tank as human factors could be minimized by this device.

scholarly journals The Glossaryfication Web Service – an automated glossary creation tool to support One Health communication

2021 ◽  
Vol 4 ◽  
Author(s):  
Estibaliz Lopez de Abechuco ◽  
Nazareno Scaccia ◽  
Taras Günther ◽  
Matthias Filter
Keyword(s):  
Web Service ◽  
Language Processing ◽  
One Health ◽  
Text Processing ◽  
Added Value ◽  
Web Interface ◽  
Source Information ◽  
Text Type ◽  
Tag Cloud ◽  
The Web

Efficient communication and collaboration across sectors is an important precondition for true One Health Surveillance (OHS) activities. Despite the overall willingness to embrace the One Health paradigm, it is still challenging to accomplish this in day-to-day practice due to the differences in terminology and interpretation of sector-specific terms. In this sense, simple interventions like the inclusion of integrative glossaries in OHS documents (e.g. reports, research papers and guidelines) would help to reduce misunderstandings and could significantly improve the written communication in OHS. Here, we present the Glossaryfication Web Service that generates a document-specific glossary for any text file provided by the user. The web service automatically adds the available definitions with their corresponding references for the words in the document that match with terms in the user-selected glossaries. The Glossaryfication Web Service was developed to provide added value to the OHEJP Glossary that was developed within the OHEJP project ORION. The OHEJP Glossary improves the communication and collaboration among OH sectors by providing an online resource that lists relevant OH terms and sector-specific definitions. The Glossaryfication Web Service supports the practical use of the curated OHEJP Glossary and can also source information from other glossaries relevant for OH professionals (currently supporting the online CDC, WHO and EFSA glossaries). The Glossaryfication Web Service was created using the open-source software KNIME and the KNIME Text Processing extension (https://www.knime.com/knime-text-processing). The Glossaryfication KNIME workflow is deployed on BfR’s KNIME Server infrastructure providing an easy-to-use web interface where the users can upload their documents (any text-type file e.g. PDF, Word, Excel) and select the desired glossary to compare with. The Glossaryfication KNIME workflow reads in the document provided via the web interface and applies natural language processing (e.g. text cleaning, stemming), transforming (bag-of-words generation) and information retrieval methods to identify the matching terms in the selected glossaries. The Glossaryfication Web Service generates as an output a table containing all the terms that match with the selected glossaries. It also provides the available definitions, corresponding references and additional meta-information, e.g. the term frequency, i.e., how often each term appears in the given text, and the sectoral classification (only for the OHEJP Glossary terms). Furthermore, the workflow generates a tag cloud where the terms are categorized as: (i) exact match when the term in the text matches exactly with the entry of this term in the glossary; (ii) inexact match when the term appears in the text slightly modified (e.g. plural forms or suffixes) and (iii) non-matching that corresponds to all the other words appearing in the text that do not match with any glossary term. Through the user interface, the users can then choose if they want to download the whole list of terms, select only the exact/inexact matching terms, or just choose those terms and definitions that match with the meaning intended for this term in the user-provided document. The resulting table of terms can be downloaded as an Excel file and added to the user’s document as a document-specific glossary. The Glossaryfication Web Service provides an easy-to-adopt solution to enrich documents and reports with more comprehensive and unambiguous glossaries. Furthermore, it improves the referentiality of terms and definitions from different OH sectors. An additional feature provided by the Glossaryfication Web Service is the possibility of extending its use to other glossaries from other national or international institutions allowing the user to customize this glossary creation service.

scholarly journals 3DNOW: IMAGE-BASED 3D RECONSTRUCTION AND MODELING VIA WEB

2018 ◽  
Vol XLII-2 ◽  
pp. 1097-1103 ◽  
Author(s):  
Y. Tefera ◽  
F. Poiesi ◽  
D. Morabito ◽  
F. Remondino ◽  
E. Nocerino ◽  
...  
Keyword(s):  
Web Service ◽  
3D Imaging ◽  
Point Clouds ◽  
Web Interface ◽  
Web Browser ◽  
Web Based ◽  
Computational Performance ◽  
Dense Point ◽  
Mesh Models ◽  
The Web

This paper presents a web-based 3D imaging pipeline, namely 3Dnow, that can be used by anyone without the need of installing additional software other than a browser. By uploading a set of images through the web interface, 3Dnow can generate sparse and dense point clouds as well as mesh models. 3D reconstructed models can be downloaded with standard formats or previewed directly on the web browser through an embedded visualisation interface. In addition to reconstructing objects, 3Dnow offers the possibility to evaluate and georeference point clouds. Reconstruction statistics, such as minimum, maximum and average intersection angles, point redundancy and density can also be accessed. The paper describes all features available in the web service and provides an analysis of the computational performance using servers with different GPU configurations.

DepLogo: visualizing sequence dependencies in R

2019 ◽  
Vol 35 (22) ◽  
pp. 4812-4814 ◽  
Author(s):  
Jan Grau ◽  
Martin Nettling ◽  
Jens Keilwagen
Keyword(s):  
Mutual Information ◽  
Sequence Data ◽  
Source Code ◽  
Protein Sequences ◽  
R Package ◽  
Supplementary Information ◽  
Supplementary Data ◽  
Sequence Logos ◽  
End Sequences ◽  
Dependency Structures

Abstract Summary Statistical dependencies are present in a variety of sequence data, but are not discernible from traditional sequence logos. Here, we present the R package DepLogo for visualizing inter-position dependencies in aligned sequence data as dependency logos. Dependency logos make dependency structures, which correspond to regular co-occurrences of symbols at dependent positions, visually perceptible. To this end, sequences are partitioned based on their symbols at highly dependent positions as measured by mutual information, and each partition obtains its own visual representation. We illustrate the utility of the DepLogo package in several use cases generating dependency logos from DNA, RNA and protein sequences. Availability and implementation The DepLogo R package is available from CRAN and its source code is available at https://github.com/Jstacs/DepLogo. Supplementary information Supplementary data are available at Bioinformatics online.

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