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Web server

About: Web server is a(n) research topic. Over the lifetime, 29784 publication(s) have been published within this topic receiving 564837 citation(s).

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Journal ArticleDOI
Michael Zuker1Institutions (1)
TL;DR: The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large by making use of universally available web GUIs (Graphical User Interfaces).

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Abstract: The abbreviated name,‘mfold web server’,describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of universally available web GUIs (Graphical User Interfaces),the server circumvents the problem of portability of this software. Detailed output,in the form of structure plots with or without reliability information,single strand frequency plots and ‘energy dot plots’, are available for the folding of single sequences. A variety of ‘bulk’ servers give less information,but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is http://www.bioinfo.rpi.edu/applications/ mfold. This URL will be referred to as ‘MFOLDROOT’.

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11,636 citations


Journal ArticleDOI
Xavier Robert1, Patrice Gouet1Institutions (1)
TL;DR: This major upgrade has been fully re-engineered to enhance speed, accuracy and usability with interactive 3D visualization of ENDscript 2 and ESPript 3 to handle a large number of data with reduced computation time.

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Abstract: ENDscript 2 is a friendly Web server for extracting and rendering a comprehensive analysis of primary to quaternary protein structure information in an automated way. This major upgrade has been fully re-engineered to enhance speed, accuracy and usability with interactive 3D visualization. It takes advantage of the new version 3 of ESPript, our well-known sequence alignment renderer, improved to handle a large number of data with reduced computation time. From a single PDB entry or file, ENDscript produces high quality figures displaying multiple sequence alignment of proteins homologous to the query, colored according to residue conservation. Furthermore, the experimental secondary structure elements and a detailed set of relevant biophysical and structural data are depicted. All this information and more are now mapped on interactive 3D PyMOL representations. Thanks to its adaptive and rigorous algorithm, beginner to expert users can modify settings to fine-tune ENDscript to their needs. ENDscript has also been upgraded as an open platform for the visualization of multiple biochemical and structural data coming from external biotool Web servers, with both 2D and 3D representations. ENDscript 2 and ESPript 3 are freely available at http://endscript.ibcp.fr and http://espript.ibcp.fr, respectively.

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3,493 citations


Journal ArticleDOI
Zefang Tang1, Chenwei Li1, Boxi Kang1, Ge Gao1  +2 moreInstitutions (1)
TL;DR: GEPIA (Gene Expression Profiling Interactive Analysis) fills in the gap between cancer genomics big data and the delivery of integrated information to end users, thus helping unleash the value of the current data resources.

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Abstract: Tremendous amount of RNA sequencing data have been produced by large consortium projects such as TCGA and GTEx, creating new opportunities for data mining and deeper understanding of gene functions. While certain existing web servers are valuable and widely used, many expression analysis functions needed by experimental biologists are still not adequately addressed by these tools. We introduce GEPIA (Gene Expression Profiling Interactive Analysis), a web-based tool to deliver fast and customizable functionalities based on TCGA and GTEx data. GEPIA provides key interactive and customizable functions including differential expression analysis, profiling plotting, correlation analysis, patient survival analysis, similar gene detection and dimensionality reduction analysis. The comprehensive expression analyses with simple clicking through GEPIA greatly facilitate data mining in wide research areas, scientific discussion and the therapeutic discovery process. GEPIA fills in the gap between cancer genomics big data and the delivery of integrated information to end users, thus helping unleash the value of the current data resources. GEPIA is available at http://gepia.cancer-pku.cn/.

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3,491 citations


Journal ArticleDOI
Robert D. Finn1, Jody Clements1, Sean R. Eddy1Institutions (1)
TL;DR: This work has focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them.

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Abstract: HMMER is a software suite for protein sequence similarity searches using probabilistic methods Previously, HMMER has mainly been available only as a computationally intensive UNIX command-line tool, restricting its use Recent advances in the software, HMMER3, have resulted in a 100-fold speed gain relative to previous versions It is now feasible to make efficient profile hidden Markov model (profile HMM) searches via the web A HMMER web server (http://hmmerjaneliaorg) has been designed and implemented such that most protein database searches return within a few seconds Methods are available for searching either a single protein sequence, multiple protein sequence alignment or profile HMM against a target sequence database, and for searching a protein sequence against Pfam The web server is designed to cater to a range of different user expertise and accepts batch uploading of multiple queries at once All search methods are also available as RESTful web services, thereby allowing them to be readily integrated as remotely executed tasks in locally scripted workflows We have focused on minimizing search times and the ability to rapidly display tabular results, regardless of the number of matches found, developing graphical summaries of the search results to provide quick, intuitive appraisement of them

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3,277 citations


Journal ArticleDOI
Fidel Ramírez1, Devon Ryan1, Björn Grüning2, Vivek Bhardwaj1  +5 moreInstitutions (3)
TL;DR: An update to the Galaxy-based web server deepTools, which allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches, is presented.

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Abstract: We present an update to our Galaxy-based web server for processing and visualizing deeply sequenced data. Its core tool set, deepTools, allows users to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches. Since we first described our deepTools Galaxy server in 2014, we have implemented new solutions for many requests from the community and our users. Here, we introduce significant enhancements and new tools to further improve data visualization and interpretation. deepTools continue to be open to all users and freely available as a web service at deeptools.ie-freiburg.mpg.de The new deepTools2 suite can be easily deployed within any Galaxy framework via the toolshed repository, and we also provide source code for command line usage under Linux and Mac OS X. A public and documented API for access to deepTools functionality is also available.

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2,563 citations


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Performance
Metrics
No. of papers in the topic in previous years
YearPapers
20222
2021270
2020552
2019818
2018844
2017949

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Topic's top 5 most impactful authors

Leszek Borzemski

24 papers, 162 citations

Tarek Abdelzaher

19 papers, 1.9K citations

Grażyna Suchacka

17 papers, 97 citations

Arun Iyengar

13 papers, 723 citations

Krzysztof Zatwarnicki

13 papers, 81 citations