Alignment-free models in plant genomics theoretical, experimental and legal issues by Humberto GonzГЎlez-DГ­az

Cover of: Alignment-free models in plant genomics | Humberto GonzГЎlez-DГ­az

Published by Nova Science in New York .

Written in English

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Subjects:

  • Mathematical models,
  • Bioinformatics,
  • Plant genome mapping,
  • QSAR (Biochemistry)

Edition Notes

Includes bibliographical references (p. [55]-70) and index.

Book details

StatementHumberto González-Díaz ... [et al.].
SeriesAgriculture issues and policies, Agriculture issues and policies series
Classifications
LC ClassificationsQK981.45 .A45 2010
The Physical Object
Pagination78 p. :
Number of Pages78
ID Numbers
Open LibraryOL25095316M
ISBN 101616683333
ISBN 109781616683337
LC Control Number2011293052
OCLC/WorldCa620341724

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Alignment-Free Models in Plant Genomics: Theoretical, Experimental, and Legal Issues (Agriculture Issues and Policies) UK ed. Edition by Humberto Gonzalez-diaz (Author), Guillermin Aguero-chapin (Author), Cristian Robert Munteanu (Author), Francisco Prado-prado (Author), Kuo-Chen Chou (Author) & 2 moreAuthor: H.

González-Díaz, G. Ag{̈u}ero-Chapin, C. Munteanu, F. Prado-Prado, K.-C. Chou, A. Duardo-Sanchez. - Buy Alignment-Free Models in Plant Genomics: Theoretical, Experimental & Legal Issues (Agriculture Issues and Policies) book online at best prices in India on Read Alignment-Free Models in Plant Genomics: Theoretical, Experimental & Legal Issues (Agriculture Issues and Policies) book reviews & author details and more at Free delivery on Author: Humberto Gonzalez-Diaz, Guillermin Aguero-Chapin, Cristian Robert Munteanu.

Alignment-free models in plant genomics: Theoretical, experimental, and legal issues Chapter   January   with  7 Reads  How we measure 'reads' A 'read' is counted each time someone views.

From this book it is possible to conclude that MARCH-INSIDE models may be applied in Plant Genomics and Biotechnology to find new interesting enzymes without relying upon alignment techniques.

Semantic Scholar extracted view of "Alignment-Free Models in Plant Genomics: Theoretical, Experimental, and Legal Issues" by Humberto González-Díaz et al. Plant genomics is a growing and constantly evolving field of study, one which has gained much ground in past years through the development of advanced research and data management tools.

In Plant Genomics: Methods and Protocols, expert researchers explore the current issues and methodologies of. Alignment-free (AF) sequence comparison is attracting persistent interest driven by data-intensive applications. Hence, many AF procedures Alignment-free models in plant genomics book been proposed in recent years, but a lack of a clearly defined benchmarking consensus hampers their performance assessment.

particularly in molecular biology and genomics. It is the first and key. Most models in Kipoi developed for animal or human genomes can be easily retrained using plant genomics datasets, or even applied directly on plants (such as models predicting biochemical properties of proteins); however, care must be taken when the biological question being studied involves plant-specific problems.

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Epigenetics and Human Health. Fungal Biology. Biotechnology in Agriculture and Forestry. Nucleic Acids and Molecular Biology. SpringerBriefs in. In bioinformatics, alignment-free sequence analysis approaches to molecular sequence and structure data provide alternatives over alignment-based approaches.

The emergence and need for the analysis of different types of data generated through biological research has given rise to the field of bioinformatics. Molecular sequence and structure data of DNA, RNA, and proteins, gene expression.

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The March-Inside approach is a computational method that can be used to seek Quantitative Structure-Property Relationships (QSAR) models in genes and their product RNA and/or proteins without to rely upon sequence alignment.

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This is a timely review which highlights the recent finding of frequent gene and whole genome duplication. DAVID J. BALDING, PhD, is Professor of Statistical Genetics at the University of Melbourne and holds an honorary appointment at University College London.

IDA MOLTKE, PhD, is an Assistant Professor at the Department of Biology, University of Copenhagen. JOHN MARIONI, PhD, is a Group Leader at the European Bioinformatics Institute and the Cancer Research UK Cambridge Institute.

Introduction to basic procedures in plant biotechnology; Gene structure and isolation. Control of gene expression and silencing. Protein targeting and expression. Plant genomics and transcriptomics. Plant proteomics. Plant metabolomics. Other omics.

Genome sequencing, models for developing synteny maps. Andrew H. Paterson, Ph.D. is a Distinguished Research Professor at the University of Georgia, jointly appointed in three Departments (Crop and Soil Science, Plant Biology, and Genetics) and the director of the Plant Genome Mapping Laboratory ().

He has authored or co-authored refereed publications, 53 book chapters, 6. Alignment-free models in plant genomics theoretical, experimental, and legal issues / Published: ().

Plant Genetics and Genomics: Crops and Models Series Editor: Richard A. Jorgensen Forthcoming and planned volumes Vol. 1 Genomics of Tropical Crop Plants (eds: Paul Moore/Ray Ming) Vol. 2 Genetics and Genomics of Soybean (ed: Gary Stacey) Vol. 3 Genetics and Genomics of.

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The AAF method is a robust tool for phylogeny reconstruction especially when only low-coverage and heterogeneous genome data are available. This application was developed, explained, and validated using a combination of sequence evolution models, mathematical calculations and.

Sequence-indexed insertional libraries are important resources for functional gene study in model plants.

However, the maize (Zea mays) UniformMu library covers only 36% of the annotated maize genes. Here, we generated a new sequence-indexed maize Mutator insertional library named ChinaMu through high-throughput sequencing of enriched Mu -tagged sequences.

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With the completion of the Arabidopsis genome sequencing project, the next major challenge is the large-scale determination of gene function. As a model organism for agricultural biotechnology, Arabidopsis presents the opportunity to provide key insights into the way that gene function can affect commercial crop production.

In an attempt to aid in the rapid discovery of gene function, we have. Previous work on alignment-free statistics. The first alignment-free method was proposed by Blaisdell in Let X and Y be two sequences from an alphabet Σ, for a given k, the value X w is the number of times w appears in X, with possible overlaps.

The D 2 statistic is defined as: D 2 = ∑ w∈Σ k X w Y w. Abiotic stresses are among the principal limiting factors for productivity in agriculture. In the current era of continuous climate changes, the understanding of the molecular aspects involved in abiotic stress response in plants is a priority.

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For comparison of whole-genome (genic + nongenic) sequences, multiple sequence alignment of a few selected genes is not appropriate. One approach is to use an alignment-free method in which feature (or l -mer) frequency profiles (FFP) of whole genomes are used for comparison—a variation of a text or book comparison method, using word frequency profiles.

Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for next-generation sequencing data processing and analysis.

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