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The MPI bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis

Vikram Alva, Seung-Zin Nam, Johannes Söding, Andrei N. Lupas
2016 Nucleic Acids Research  
The MPI Bioinformatics Toolkit (http://toolkit. tuebingen.mpg.de) is an open, interactive web service for comprehensive and collaborative protein bioinformatic analysis.  ...  In fact, through the breadth of its tools and their tight interconnection, the Toolkit has become an excellent platform for experimental scientists as well as a useful resource for teaching bioinformatic  ...  Toolkit over the years, as well as our current undergraduate students working on the Toolkit: Andrew Stephens, Jonas Kübler and Lukas Zimmermann.  ... 
doi:10.1093/nar/gkw348 pmid:27131380 pmcid:PMC4987908 fatcat:ffsm76krd5hhvctyfgr5gnu4ne

The MIGenAS integrated bioinformatics toolkit for web-based sequence analysis

M. Rampp, T. Soddemann, H. Lederer
2006 Nucleic Acids Research  
We describe a versatile and extensible integrated bioinformatics toolkit for the analysis of biological sequences over the Internet.  ...  Currently, supported tasks comprise sequence similarity searches in public or usersupplied databases, computation and validation of multiple sequence alignments, phylogenetic analysis and protein-structure  ...  ACKNOWLEDGEMENTS We are indebted to the members of the MIGenAS consortium for sharing their software and expertise with us.  ... 
doi:10.1093/nar/gkl254 pmid:16844980 pmcid:PMC1538907 fatcat:5a5hnmrfzvdhxiiaon4istz6um

The role of high performance, grid and cloud computing in high-throughput sequencing

Gaye Lightbody, Fiona Browne, Huiru Zheng, Valeriia Haberland, Jaine Blayney
2016 2016 IEEE International Conference on Bioinformatics and Biomedicine (BIBM)  
This paper provides an overview of the evolution of high-throughput sequencing and the tools, infrastructure and data management developing in this space to support a key area in personalized medicine.  ...  The paper concludes by providing an outlook in the future of such technologies and their applications and how they might shape clinical governance.  ...  It has been used to measure transcription binding and protein interactions. miRNA-Seq NGS (Next Generation Sequencing, a form of HTS) technology has been an enabler for analysis of transcriptomes [16]  ... 
doi:10.1109/bibm.2016.7822643 dblp:conf/bibm/LightbodyBZHB16 fatcat:emjxedmvrnfshdtrynakwurl4q

Emergence of in-silico biology in desperate spheres of life sciences in Pakistan

Muhammad Naveed
2019 Pure and Applied Biology  
Bioinformatics, a multidisciplinary field works in collaboration with biological sciences for analysis, prediction and storage of biological data in form of databases.  ...  tools: AJ Iqbal & M Naveed, Wrote the paper: H Sadia, M Amin & S Asif. bioinformatics Toolkit as an integrative platform for advanced protein sequence and structure analysis.  ...  Bioinformatics is often confused with Bio computation or Compactional Biology. The MPI (http://toolkit.tuebingen.mpg.de) analyses protein sequence and its structural features.  ... 
doi:10.19045/bspab.2019.80004 fatcat:uo3ghca4mjdoxpjulbqxentax4

Web and Grid Technologies in Bioinformatics, Computational and Systems Biology: A Review

Natalio Krasnogor, Azhar Shah, Daniel Barthel, Piotr Lukasiak, Jacek Blazewicz
2008 Current Bioinformatics  
Furthermore, the proliferation of biotechnologies and advances in biological sciences has produced a strong drive for new informatics solutions, both at the basic science and technological levels.  ...  //www.gmod.org/home An integrated organism database PSI-MI [56] Proteomics Standards Initiative: Molecular Interactions http://psidev.sourceforge.net/ Data standard for proteomics  ...  Similarly, the gridification of other applications such as a grid-enabled bioinformatics portal for protein sequence analysis, grid-enabled method for securely finding unique sequences for PCR primers,  ... 
doi:10.2174/157489308783329850 fatcat:thpj6eywwvg5tfdqvbw5nch3ty

Workflow management systems for gene sequence analysis and evolutionary studies – A Review

Anu Sharma, Anil Rai, SB Lal
2013 Bioinformation  
This article describes the bioinformatics analysis workflow management systems that are developed in the area of gene sequence analysis and phylogeny.  ...  Building integrated bioinformatics platforms is one of the most challenging tasks that bioinformatics community is facing.  ...  Protein Annotation Toolkit (PAT) [6] is an integrated bio-computing server that provides a standardized web interface to a wide range of protein analysis tools.  ... 
doi:10.6026/97320630009663 pmid:23930017 pmcid:PMC3732438 fatcat:rln37g5m65ekfph5alpidk7dei

A Review on Design and Development of Performance Evaluation Model for Bio-Informatics Data Using Hadoop

Ravi Kumar A, Et. al.
2021 Turkish Journal of Computer and Mathematics Education  
The paper reviews the usage of the platform Hadoop in applications for systemic bioinformatics.  ...  Hadoop offers another system for Structural Bioinformatics to break down broad fractions of the Protein Data Bank that is crucial to high-throughput investigations of (for example) protein-ligand docking  ...  the relevance of computationally analysing protein structures in fields such as membrane proteins, protein-protein interactions, and their effect in system biology and protein architecture of a platform  ... 
doi:10.17762/turcomat.v12i2.1432 fatcat:bnake6gvsrfytov5axuiwmvjpu

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

Sander Pronk, Szilárd Páll, Roland Schulz, Per Larsson, Pär Bjelkmar, Rossen Apostolov, Michael R. Shirts, Jeremy C. Smith, Peter M. Kasson, David van der Spoel, Berk Hess, Erik Lindahl
2013 Computer applications in the biosciences : CABIOS  
The distribution automatically handles wide classes of biomolecules such as proteins, nucleic acids, and lipids and comes with all commonly used force fields for these molecules built-in.  ...  At the same time, advances in scaling now make it possible to model complex protein motion and function in a manner directly testable by experiment.  ...  ACKNOWLEDGEMENTS The authors would particularly like to thank Marten Wolf and Gerrit Groenhof for contributing the g membed tool that has addressed the long-standing issue of solvating proteins in membranes  ... 
doi:10.1093/bioinformatics/btt055 pmid:23407358 pmcid:PMC3605599 fatcat:e24ivcsvbbeo3csscb22hujfze

ToolsAU

Maria Victoria Schneider, MADISON FLANNERY
2017 Figshare  
EMBL-ABR ToolsAU, powered by the ELIXIR Tools and Data Service Registry  ...  ., is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data.  ...  Short Linear Motif discovery and molecular evolution toolkit SLiMSuite is an open source suite of Python programs for sequence analysis, with a particular focus on the prediction and analysis of short  ... 
doi:10.6084/m9.figshare.5011793.v1 fatcat:vsflwotpr5hypa564avdbywn5y

Next Generation Distributed Computing for Cancer Research

Pankaj Agarwal, Kouros Owzar
2014 Cancer Informatics  
Advances in next generation sequencing (NGS) and mass spectrometry (MS) technologies have provided many new opportunities and angles for extending the scope of translational cancer research while creating  ...  A proof-of-concept Hadoop cluster, set up for performance benchmarking of NGS read alignment, is described as an example of how to work with Hadoop.  ...  Acknowledgment The authors thank the reviewers for insightful and helpful comments.  ... 
doi:10.4137/cin.s16344 pmid:25983539 pmcid:PMC4412427 fatcat:wpjhyuakejhirekbzouxtjdqnu

ScalaBLAST: A Scalable Implementation of BLAST for High-Performance Data-Intensive Bioinformatics Analysis

C. Oehmen, J. Nieplocha
2006 IEEE Transactions on Parallel and Distributed Systems  
For each genome sequenced, the challenge is to identify protein components (proteome) being actively used for a given set of conditions.  ...  Genes in an organism's DNA (genome) have embedded in them information about proteins, which are the molecules that do most of a cell's work.  ...  For our benchmark data set, ScalaBLAST scales significantly better than MPI-BLAST and performs as well as HTC-BLAST in terms of runtime for real-world queries against the nonredundant protein database  ... 
doi:10.1109/tpds.2006.112 fatcat:opc5wcewlvhc7nc3eewduamydu

Parallel computing in genomic research: advances and applications

Daniel de Oliveira, Kary Ocaña
2015 Advances and Applications in Bioinformatics and Chemistry  
However, running bioinformatics experiments in HPC environments such as clouds, grids, clusters, and graphics processing unit requires the expertise from scientists to integrate computational, biological  ...  Parallelism techniques and high-performance computing (HPC) environments can be applied for reducing the total processing time and to ease the management, treatment, and analyses of this data.  ...  Author contributions All authors contributed toward data analysis, drafting and revising the paper and agree to be accountable for all aspects of the work.  ... 
doi:10.2147/aabc.s64482 pmid:26604801 pmcid:PMC4655901 fatcat:qyslams5evftjm7euma5vg2rtq

Bioinformatics Tools for Crop Research and Breeding [chapter]

B Jayashree, Dave Hoisington
2009 Molecular Techniques in Crop Improvement  
the effective analysis, data mining and visualization of such information; and semantic web resources for data integration.  ...  In this chapter, we highlight the role and contributions of bioinformatics to crop research and breeding by focusing on the bioinformatics resources that are available for crop science research and breeding  ...  The Lagan Toolkit is a set of alignment programs for comparative genomics (Brudno et al. 2003) while the Staden Package is a suite of tools for sequence assembly, analysis, and mutation detection (Staden  ... 
doi:10.1007/978-90-481-2967-6_4 fatcat:aua2644ikrez5hmuemxybom4lq

A Maintainable Software Architecture for Fast and Modular Bioinformatics Sequence Search

Jeremy Archuleta, Eli Tilevich, Wu-chun Feng
2007 Conference on Software Maintenance, Proceedings of the  
design by precipitating flexible and structured parallel development, a necessity for an open-source application.  ...  Bioinformaticists use the Basic Local Alignment Search Tool (BLAST) to characterize an unknown sequence by comparing it against a database of known sequences, thus detecting evolutionary relationships  ...  Acknowledgments We would like to thank Shawn Bohner, Spencer Rugaber, Yannis Smaragdakis, and the anonymous reviewers whose comments have helped to improve this paper.  ... 
doi:10.1109/icsm.2007.4362627 dblp:conf/icsm/ArchuletaTF07 fatcat:4fvooqmsrfdzhkxynokylrulkq

Distributed Computing in a Pandemic: A Review of Technologies Available for Tackling COVID-19 [article]

Jamie J Alnasir
2021 arXiv   pre-print
drug-repurposing, and high-throughput gene analysis -- and Sentinel, an XPE-Cray based system used to explore natural products.  ...  computing devices using the Folding@home platform.  ...  Cloud Computing A consequence of the data-driven, integrative nature of bioinformatics and computational biology [87] , as well as advancements in high-throughput next-generation sequencing [88] , is  ... 
arXiv:2010.04700v3 fatcat:kxakuqjlyjfilbroj5nl55xgbq
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