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Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming

Ignacio L. Ibarra, Francisco Melo
2010 Computer applications in the biosciences : CABIOS  
In bioinformatics, it is widely applied in calculating the optimal alignment between pairs of protein or DNA sequences. These alignments form the basis of new, verifiable biological hypothesis.  ...  The program displays the DP scoring matrix and the resulting optimal alignment(s), while allowing the user to modify key parameters such as the values in the similarity matrix, the sequence alignment algorithm  ...  ACKNOWLEDGEMENTS The authors would like to thank Javier Castellanos, Alex Slater and Tomás Norambuena for helpful discussions. We are also grateful to Drs Manfred Sippl, Andrej Sali, M.S.  ... 
doi:10.1093/bioinformatics/btq252 pmid:20472540 pmcid:PMC2887054 fatcat:nxg4bevsqze55bw3flvs7dnldu

PoSE: visualization of patterns of sequence evolution using PAML and MATLAB

Kun Zhao, Elizabeth Henderson, Kelley Bullard, M. Steven Oberste, Cara C. Burns, Jaume Jorba
2018 BMC Bioinformatics  
The application displays inferred substitutions estimated by baseml or codeml, two programs included in the PAML software package.  ...  However, it is not easy to visualize the different phylogenetic signatures imprinted in aligned nucleotide and amino acid sequences.  ...  Acknowledgments The authors would like to thank Ms. Anita Gajjala (Mathworks) for her technical assistance on MATLAB coding.  ... 
doi:10.1186/s12859-018-2335-7 fatcat:xdpx2yv6c5ahxklcnsnrencjpq

Bioinformatics: A Way Forward to Explore "Plant Omics" [chapter]

Mehboob-ur Rahman, Tayyaba Shaheen, Mahmood-ur Rahman, Muhammad Atif Iqbal, Yusuf Zafar
2016 Bioinformatics - Updated Features and Applications  
This science has progressed parallel to the evolution of genome-sequencing tools, for example, the next-generation sequencing technologies, that resulted in arranging and analyzing the genome-sequencing  ...  In future, inventions of high-tech computational tools and skills together with improved biological expertise would provide better insight into the genomes, and this information would be helpful in sustaining  ...  A number of algorithms are available to generate MSA of proteins and DNA sequences. The basic approach in producing multiple alignments is to optimize the sum of pairs (SP) score.  ... 
doi:10.5772/64043 fatcat:w3cwexdezvf27e5adz3gfos4v4

Scenariographer: a tool for reverse engineering class usage scenarios from method invocation sequences

M. Salah, T. Denton, S. Mancoridis, A. Shokoufandeh, F.I. Vokolos
2005 21st IEEE International Conference on Software Maintenance (ICSM'05)  
Knowing the sequence with which methods of a class can be invoked is useful information especially for software engineers (e.g., developers, testers) who are actively involved in the maintenance of large  ...  sequence < open, close >, which can be used to check the existence of a file.  ...  source code analysis, software clustering, dynamic analysis of software execution, profiling, program slicing, and visualization.  ... 
doi:10.1109/icsm.2005.78 dblp:conf/icsm/SalahDMSV05 fatcat:gy4umiytfngz3ltxmuyfy6osle

Use of Bioinformatics Tools in Different Spheres of Life Sciences

Muhammad Aamer Mehmood
2014 Journal of Data Mining in Genomics & Proteomics  
Acknowledgment Authors thank Higher Education Commission (HEC), Pakistan, for funding their research work and apologise to all those colleagues whose work could not be discussed here due to space constraints  ...  [123] TreeView Software to view the phylogenetic trees, with the provision of changing view.  ...  [109] HMMER Homologous protein sequences may be searched from the respective databases using this tool. [110] Clustal Omega Multiple sequence alignments may be performed using this program.  ... 
doi:10.4172/2153-0602.1000158 fatcat:m5ziueg3ifaobfnovyguaqlixa

Survey of Natural Language Processing Techniques in Bioinformatics

Zhiqiang Zeng, Hua Shi, Yun Wu, Zhiling Hong
2015 Computational and Mathematical Methods in Medicine  
Then, we analyze the applications of text mining and natural language processing techniques in bioinformatics, including predicting protein structure and function, detecting noncoding RNA.  ...  For example, protein-protein interactions and gene-disease relationship can be mined from PubMed.  ...  Introduction Text mining and natural language processing refer to comprehending and analyzing natural language by using computer algorithms and programs.  ... 
doi:10.1155/2015/674296 pmid:26525745 pmcid:PMC4615216 fatcat:z4txhlt4jfhmtlaje4mbrdnxme

ProteinShop: A tool for interactive protein manipulation and steering

Silvia Crivelli, Oliver Kreylos, Bernd Hamann, Nelson Max, Wes Bethel
2004 Journal of Computer-Aided Molecular Design  
ProteinShop makes it possible, when used in combination with an optimization system, to interact with and guide the numerical optimization process.  ...  The problem is compounded by the presence of β-strands for which there is a combinatorial number of possible strand alignments, each of which needs to be created with a different constrained minimization  ...  In this paper we present ProteinShop, an interactive visualization and molecular manipulation tool designed to permit users to determine optimal tertiary structure of proteins based on an initial sequence  ... 
doi:10.1023/b:jcam.0000046822.54719.4f pmid:15562991 fatcat:shma2duprfayneokkpvs2k26wm

Intelligent mining of large-scale bio-data: Bioinformatics applications

Farahnaz Sadat Golestan Hashemi, Mohd Razi Ismail, Mohd Rafii Yusop, Mahboobe Sadat Golestan Hashemi, Mohammad Hossein Nadimi Shahraki, Hamid Rastegari, Gous Miah, Farzad Aslani
2017 Biotechnology & Biotechnological Equipment  
Hence, there is a high potential to raise the interaction between artificial intelligence and bio-data mining.  ...  The present paper argues how artificial intelligence can assist bio-data analysis and gives an up-to-date review of different applications of bio-data mining.  ...  Type of pairwise alignment Algorithm Characteristics References Optimal Local Smith-Waterman Dynamic programming [30] Global Needleman-Wunch Dynamic programming [37] Heuristic ). sensitive  ... 
doi:10.1080/13102818.2017.1364977 fatcat:qmbiss53wfggtc7ayj2ysgt5rq

Mutation Based Structural Modelling and Dynamics Study of Alpha Fetoprotein: An Insight to Inhibitory Mechanism in Breast Cancer

Priyam Patel, Pritam Kumar Panda, Sneha Patil, Hetalkumar Panchal
2018 Journal of Proteomics & Bioinformatics  
The user provides an alignment of a sequence to be modelled with known related structures and MODELLER automatically calculates a model containing all non-hydrogen atoms.  ...  of various models of protein structure with respect to a flexibly defined objective function, multiple alignment of protein sequences and/or structures, clustering, searching of sequence databases, comparison  ... 
doi:10.4172/jpb.1000462 fatcat:izg7hgdp6nfa5intqxpdlf5aea

Scalable Genomics with R and Bioconductor

Michael Lawrence, Martin Morgan
2014 Statistical Science  
We demonstrate the strategies by applying Bioconductor packages to the detection and analysis of genetic variants from a whole genome sequencing experiment.  ...  We treat the scalable processing, summarization and visualization of big genomic data.  ...  Generating plots dynamically The design of interactive graphics software typically follows the model-view-controller pattern (see Figure 4 ).  ... 
doi:10.1214/14-sts476 pmid:28018047 pmcid:PMC5181792 fatcat:rwgbq2kqjzfk5ls44nun23spny

QuickRNASeq lifts large-scale RNA-seq data analyses to the next level of automation and interactive visualization

Shanrong Zhao, Li Xi, Jie Quan, Hualin Xi, Ying Zhang, David von Schack, Michael Vincent, Baohong Zhang
2016 BMC Genomics  
The seamless integration of automated capabilites with interactive visualizations in QuickRNASeq is not available in other published RNA-seq pipelines.  ...  In Step #1, each individual sample is processed, including mapping RNA-seq reads to a reference genome, counting the numbers of mapped reads, quality control of the aligned reads, and SNP (single nucleotide  ...  The development of QuickRNASeq was motivated partially by large scale in-house RNA sequencing projects in which thousands of samples were sequenced and analyzed.  ... 
doi:10.1186/s12864-015-2356-9 pmid:26747388 pmcid:PMC4706714 fatcat:wjekoa72ozdv3hj2mk5ub3vqyy

Bhageerath-H: A homology/ab initio hybrid server for predicting tertiary structures of monomeric soluble proteins

B Jayaram, Priyanka Dhingra, Avinash Mishra, Rahul Kaushik, Goutam Mukherjee, Ankita Singh, Shashank Shekhar
2014 BMC Bioinformatics  
The advent of human genome sequencing project has led to a spurt in the number of protein sequences in the databanks.  ...  With dwindling similarities of query sequences, advanced homology/ ab initio hybrid approaches are being explored to solve structure prediction problem.  ...  The tool requires list of protein decoys to cluster.  ... 
doi:10.1186/1471-2105-15-s16-s7 pmid:25521245 pmcid:PMC4290660 fatcat:qfauqfog45d2zjcra6ixymlsvi

Evaluation system and web infrastructure for the second cryo-EM model challenge

Andriy Kryshtafovych, Paul D. Adams, Catherine L. Lawson, Wah Chiu
2018 Journal of Structural Biology  
The evaluation system includes tools to validate stereo-chemical plausibility of submitted models, check their fit to the corresponding density maps, estimate their overall and perresidue accuracy, and  ...  It includes interactively sortable tables of evaluation scores for different subsets of models and different sublevels of structure organization, and a suite of visualization tools facilitating model analysis  ...  Joseph (TEMPy) for providing their software for the cryo-EM model challenge evaluation, for the help in adjusting the software to the needs of the EMMC evaluation and for discussing details of their tools  ... 
doi:10.1016/j.jsb.2018.07.006 pmid:30017700 pmcid:PMC6205695 fatcat:r2hma32z25dn7ml5gvzrqhchtm

Comparative modelling of protein structure and its impact on microbial cell factories

Nuria B Centeno, Joan Planas-Iglesias, Baldomero Oliva
2005 Microbial Cell Factories  
For this reason, an introduction to comparative modeling is presented, with special emphasis on the basic concepts, opportunities and challenges of protein structure prediction.  ...  Comparative modeling is becoming an increasingly helpful technique in microbial cell factories as the knowledge of the three-dimensional structure of a protein would be an invaluable aid to solve problems  ...  Among the available software to do so it is worth mentioning: the CORALL module of WHATIF [55] and the SCWRL program [56] .  ... 
doi:10.1186/1475-2859-4-20 pmid:15989691 pmcid:PMC1183243 fatcat:j7ti552ebzgztgjkrigcrtr3ya

Multi-objective kernel mapping and scheduling for morphable many-core architectures

Nuno Neves, Rui Neves, Nuno Horta, Pedro Tomás, Nuno Roma
2016 Expert systems with applications  
A new optimization framework to maximize the performance and efficiency of morphable many-core accelerators is proposed.  ...  The devised methodology supports the co-existence of multiple optimization goals and constraints (e.g., computational performance, power, energy consumption and runtime reconfiguration overhead) by relying  ...  The last phase implements a Local Sequence Alignment based on a dynamic programming approach. Its latency depends on the number of P.  ... 
doi:10.1016/j.eswa.2015.10.004 fatcat:ce37tbgklja3bfesmj4ejrsdlq
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