A Computational Framework For Transcriptome Assembly And Annotation In Non Model Organisms

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A Computational Framework for Transcriptome Assembly and Annotation in Non-model Organisms

Author :
Publisher :
ISBN 13 :
Total Pages : 348 pages
Book Rating : 4.:/5 (925 download)

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Book Synopsis A Computational Framework for Transcriptome Assembly and Annotation in Non-model Organisms by :

Download or read book A Computational Framework for Transcriptome Assembly and Annotation in Non-model Organisms written by and published by . This book was released on 2014 with total page 348 pages. Available in PDF, EPUB and Kindle. Book excerpt: This thesis is about the development of methodologies to interrogate RNA-Seq reads derived from non-model organisms. We implemented these methodologies to generate genomic information and describe a useful resource that will promote hypothesis-driven research into the biology of V. inaequalis. In this dissertation three computational approaches are presented that enable optimization of reference-free transcriptome reconstruction. The first addresses the selection of bona fide reconstructed transcribed fragments (transfrags) from de novo transcriptome assemblies and annotation with a multiple domain co-occurrence framework. We showed that selected transfrags are functionally relevant and represented over 94% of the information derived from annotation by transference. The second approach relates to quality score based DNA-seq sub-sampling and the decription of a novel sequence similarity-derived metric for quality assessment of de novo transcriptome assemblies. A detail systematic analysis of the side effects induced by quality score based trimmings and or filtering on artefact removal and transcriptome quality is descibed.

Applications of RNA-Seq and Omics Strategies

Author : Fabio Marchi
Publisher : BoD – Books on Demand
ISBN 13 : 9535135031
Total Pages : 330 pages
Book Rating : 4.5/5 (351 download)

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Book Synopsis Applications of RNA-Seq and Omics Strategies by : Fabio Marchi

Download or read book Applications of RNA-Seq and Omics Strategies written by Fabio Marchi and published by BoD – Books on Demand. This book was released on 2017-09-13 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: The large potential of RNA sequencing and other "omics" techniques has contributed to the production of a huge amount of data pursuing to answer many different questions that surround the science's great unknowns. This book presents an overview about powerful and cost-efficient methods for a comprehensive analysis of RNA-Seq data, introducing and revising advanced concepts in data analysis using the most current algorithms. A holistic view about the entire context where transcriptome is inserted is also discussed here encompassing biological areas with remarkable technological advances in the study of systems biology, from microorganisms to precision medicine.

Genomic and Transcriptomic Studies on Non-Model Organisms

Author : Shuhua Fu
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (944 download)

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Book Synopsis Genomic and Transcriptomic Studies on Non-Model Organisms by : Shuhua Fu

Download or read book Genomic and Transcriptomic Studies on Non-Model Organisms written by Shuhua Fu and published by . This book was released on 2015 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: As the advance in high-throughput sequencing enables the generation of large volumes of genomic information, it provides researchers the opportunity to study non-model organisms even in the absence of a fully sequenced genome. The hugely advantageous progress calls for powerful sequencing assembly algorithms as these technologies also raise challenging assembly problems: (1) Some RNA products are highly expressed but others may have much lower expression level. (2) Data cannot easily be represented as linear structure, due to post-transcriptional modification like alternative splicing. (3) Conserved sequences in domains in gene families can result in assembly errors, (4) Sequencing errors due to technique limitations. Useful assembly algorithms are required to overcome the difficulties above. In these studies, there is often a need to identify similar transcripts in non-model organisms to transcripts found in related organisms. The traditional approach to address this problem is to perform de novo transcriptome assemblies to obtain predicted transcripts for these organisms and then employ similarity comparison algorithms to identify them. I observe it is possible to obtain a more complete set of similar transcripts from transcriptome assembly by making use of evolutionary information. I apply new algorithms to study non-model organisms which play an important role in applied biology. Moreover, improvement of sequencing technologies and application of current algorithms also help to study interkingdom signals between blow flies and bacteria community. With current computational tools, I annotate genomes of Proteus mirabilis and Providencia stuartii, which play an important role in bacteria-insect interaction. The study shows significant features of these strains isolated, which provides useful information to develop and test hypothesis in related interactions in insects and bacteria. The electronic version of this dissertation is accessible from http://hdl.handle.net/1969.1/155184

Development of an Extensible Computational Framework for Centralized Storage and Distributed Curation and Analysis of Genomic Data Genome-scale Metabolic Models

Download Development of an Extensible Computational Framework for Centralized Storage and Distributed Curation and Analysis of Genomic Data Genome-scale Metabolic Models PDF Online Free

Author :
Publisher :
ISBN 13 :
Total Pages : 4 pages
Book Rating : 4.:/5 (946 download)

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Book Synopsis Development of an Extensible Computational Framework for Centralized Storage and Distributed Curation and Analysis of Genomic Data Genome-scale Metabolic Models by :

Download or read book Development of an Extensible Computational Framework for Centralized Storage and Distributed Curation and Analysis of Genomic Data Genome-scale Metabolic Models written by and published by . This book was released on 2010 with total page 4 pages. Available in PDF, EPUB and Kindle. Book excerpt: The DOE funded KBase project of the Stevens group at the University of Chicago was focused on four high-level goals: (i) improve extensibility, accessibility, and scalability of the SEED framework for genome annotation, curation, and analysis; (ii) extend the SEED infrastructure to support transcription regulatory network reconstructions (2.1), metabolic model reconstruction and analysis (2.2), assertions linked to data (2.3), eukaryotic annotation (2.4), and growth phenotype prediction (2.5); (iii) develop a web-API for programmatic remote access to SEED data and services; and (iv) application of all tools to bioenergy-related genomes and organisms. In response to these goals, we enhanced and improved the ModelSEED resource within the SEED to enable new modeling analyses, including improved model reconstruction and phenotype simulation. We also constructed a new website and web-API for the ModelSEED. Further, we constructed a comprehensive web-API for the SEED as a whole. We also made significant strides in building infrastructure in the SEED to support the reconstruction of transcriptional regulatory networks by developing a pipeline to identify sets of consistently expressed genes based on gene expression data. We applied this pipeline to 29 organisms, computing regulons which were subsequently stored in the SEED database and made available on the SEED website (http://pubseed.theseed.org). We developed a new pipeline and database for the use of kmers, or short 8-residue oligomer sequences, to annotate genomes at high speed. Finally, we developed the PlantSEED, or a new pipeline for annotating primary metabolism in plant genomes. All of the work performed within this project formed the early building blocks for the current DOE Knowledgebase system, and the kmer annotation pipeline, plant annotation pipeline, and modeling tools are all still in use in KBase today.

Transcriptome De Novo Assembly, Clustering, and Annotation of Novel Transcripts

Author : Fatemeh Shaadi Pooyaei Mehr
Publisher :
ISBN 13 : 9781303536946
Total Pages : 342 pages
Book Rating : 4.5/5 (369 download)

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Book Synopsis Transcriptome De Novo Assembly, Clustering, and Annotation of Novel Transcripts by : Fatemeh Shaadi Pooyaei Mehr

Download or read book Transcriptome De Novo Assembly, Clustering, and Annotation of Novel Transcripts written by Fatemeh Shaadi Pooyaei Mehr and published by . This book was released on 2013 with total page 342 pages. Available in PDF, EPUB and Kindle. Book excerpt: Recent advances in Next Generation Sequencing (NGS) have allowed for unparalleled access to genetic information for organisms in both the functional and phylogenetic realms of biology. Analysis of the RNA transcripts of cells of organisms using Next Generation Sequencing (called RNA-seq) has opened doors for unique insights into the genomic complexity of organisms and has provided researchers with invaluable tools for analysis of function of gene products and phylogenetic relatedness. Application of this method has moved beyond model organisms. It has provided a lot of potentials, in ecological research and comparative transcriptomics, in non-model organisms. This thesis presents an overview on existing applications of RNA-seq in non-model organisms. Furthermore, it presents a new clustering design on handling the data, which led to identification of twelve new fluorescent protein isoforms in corals. In addition, de novo assembly and annotation of the data from polychaete Hermodice carunculata made possible the identification of one new phylogenetic marker and eight bioluminescent protein isoforms. Also, twelve new bilirubin-induced fluorescent proteins were identified from false moray eel Kaupichthys hyproroides. This approach can be applied on any other data.

A Novel Computational Framework for Transcriptome Analysis with RNA-seq Data

Author : Yin Hu
Publisher :
ISBN 13 :
Total Pages : 203 pages
Book Rating : 4.:/5 (869 download)

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Book Synopsis A Novel Computational Framework for Transcriptome Analysis with RNA-seq Data by : Yin Hu

Download or read book A Novel Computational Framework for Transcriptome Analysis with RNA-seq Data written by Yin Hu and published by . This book was released on 2013 with total page 203 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Virus Bioinformatics

Author : Manja Marz
Publisher : MDPI
ISBN 13 : 3039218824
Total Pages : 330 pages
Book Rating : 4.0/5 (392 download)

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Book Synopsis Virus Bioinformatics by : Manja Marz

Download or read book Virus Bioinformatics written by Manja Marz and published by MDPI. This book was released on 2020-02-21 with total page 330 pages. Available in PDF, EPUB and Kindle. Book excerpt: Virus bioinformatics is evolving and succeeding as an area of research in its own right, representing the interface of virology and computer science. Bioinformatic approaches to investigate viral infections and outbreaks have become central to virology research, and have been successfully used to detect, control, and treat infections of humans and animals. As part of the Third Annual Meeting of the European Virus Bioinformatics Center (EVBC), we have published this Special Issue on Virus Bioinformatics.

Next Generation Sequencing

Author : Jerzy Kulski
Publisher : BoD – Books on Demand
ISBN 13 : 9535122401
Total Pages : 466 pages
Book Rating : 4.5/5 (351 download)

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Book Synopsis Next Generation Sequencing by : Jerzy Kulski

Download or read book Next Generation Sequencing written by Jerzy Kulski and published by BoD – Books on Demand. This book was released on 2016-01-14 with total page 466 pages. Available in PDF, EPUB and Kindle. Book excerpt: Next generation sequencing (NGS) has surpassed the traditional Sanger sequencing method to become the main choice for large-scale, genome-wide sequencing studies with ultra-high-throughput production and a huge reduction in costs. The NGS technologies have had enormous impact on the studies of structural and functional genomics in all the life sciences. In this book, Next Generation Sequencing Advances, Applications and Challenges, the sixteen chapters written by experts cover various aspects of NGS including genomics, transcriptomics and methylomics, the sequencing platforms, and the bioinformatics challenges in processing and analysing huge amounts of sequencing data. Following an overview of the evolution of NGS in the brave new world of omics, the book examines the advances and challenges of NGS applications in basic and applied research on microorganisms, agricultural plants and humans. This book is of value to all who are interested in DNA sequencing and bioinformatics across all fields of the life sciences.

Biological Sequence Analysis

Author : Richard Durbin
Publisher : Cambridge University Press
ISBN 13 : 113945739X
Total Pages : 372 pages
Book Rating : 4.1/5 (394 download)

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Book Synopsis Biological Sequence Analysis by : Richard Durbin

Download or read book Biological Sequence Analysis written by Richard Durbin and published by Cambridge University Press. This book was released on 1998-04-23 with total page 372 pages. Available in PDF, EPUB and Kindle. Book excerpt: Probabilistic models are becoming increasingly important in analysing the huge amount of data being produced by large-scale DNA-sequencing efforts such as the Human Genome Project. For example, hidden Markov models are used for analysing biological sequences, linguistic-grammar-based probabilistic models for identifying RNA secondary structure, and probabilistic evolutionary models for inferring phylogenies of sequences from different organisms. This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis. Written by an interdisciplinary team of authors, it aims to be accessible to molecular biologists, computer scientists, and mathematicians with no formal knowledge of the other fields, and at the same time present the state-of-the-art in this new and highly important field.

Bioinformatics and Biomedical Engineering

Author : Ignacio Rojas
Publisher : Springer Nature
ISBN 13 : 3030453855
Total Pages : 843 pages
Book Rating : 4.0/5 (34 download)

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Book Synopsis Bioinformatics and Biomedical Engineering by : Ignacio Rojas

Download or read book Bioinformatics and Biomedical Engineering written by Ignacio Rojas and published by Springer Nature. This book was released on 2020-04-30 with total page 843 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume constitutes the proceedings of the 8th International Work-Conference on IWBBIO 2020, held in Granada, Spain, in May 2020. The total of 73papers presented in the proceedings, was carefully reviewed and selected from 241 submissions. The papers are organized in topical sections as follows: Biomarker Identification; Biomedical Engineering; Biomedical Signal Analysis; Bio-Nanotechnology; Computational Approaches for Drug Design and Personalized Medicine; Computational Proteomics and Protein-Protein Interactions; Data Mining from UV/VIS/NIR Imaging and Spectrophotometry; E-Health Technology, Services and Applications; Evolving Towards Digital Twins in Healthcare (EDITH); High Performance in Bioinformatics; High-Throughput Genomics: Bioinformatic Tools and Medical Applications; Machine Learning in Bioinformatics; Medical Image Processing; Simulation and Visualization of Biological Systems.

Assembly, Annotation and Polymorphism Analysis of a Draft Transcriptome Sequence for a Fast-growing Eucalyptus Plantation Tree

Author : Charles Amadeus Hefer
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.:/5 (956 download)

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Book Synopsis Assembly, Annotation and Polymorphism Analysis of a Draft Transcriptome Sequence for a Fast-growing Eucalyptus Plantation Tree by : Charles Amadeus Hefer

Download or read book Assembly, Annotation and Polymorphism Analysis of a Draft Transcriptome Sequence for a Fast-growing Eucalyptus Plantation Tree written by Charles Amadeus Hefer and published by . This book was released on 2013 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Ultra-high throughput DNA sequencing technologies have rapidly changed the face of genomic research projects. Technologies such as mRNA-Seq have the potential to rapidly profile the expressed gene-catalog of non-model organisms, albeit with significant bioinformatics related costs and support required. This study developed automated data analysis workflows focused on the quality evaluation of mRNA-Seq reads, de novo transcriptome assembly, transcriptome annotation and digital gene expression profiling making use of data analysis tools available in the public domain and novel tools developed for this purpose. The developed workflows were made available in a private instance of the Galaxy workflow management system. The developed workflows were used to perform the de novo assembly of a gene-catalog of a Eucalyptus plantation tree. The fast growing and good wood properties of Eucalyptus tree species and their hybrids make them excellent renewable resources of fiber for pulp and paper, and woody biomass for bioenergy production. We produced an expressed gene-catalog of 18 894 de novo assembled contigs from Illumina deep mRNA-Seq of six sampled plant tissues. Using a novel coverage-assisted re-assembly approach, we were able to assemble near full-length biologically relevant transcripts. The assembly was evaluated in terms of contig quality and contiguity, and functional annotations were assigned. Digital expression profiling (FPKM values) of each contig across the tissues were calculated, which was used to identify of tissue-specific sets of expressed genes. Polymorphism analysis of 13 806 high-confidence contigs revealed a combined exon and untranslated region SNP density of 0.534 SNPs/100 bp, which provides a good opportunity for designing high-density SNP assays in the expressed regions of the Eucalyptus genome. The assembled and annotated gene catalog was made available for public use in a user-friendly, web-based interface as the Eucspresso database (http://eucspresso.bi.up.ac.za). The developed database acts as a prelude to a more comprehensive mRNA-Seq whole-transcriptome repository, the Eucalyptus Genome Intergrative Explorer (EucGenIE), a resource that will focus on identifying transcriptional networks active during woody biomass development. Results from the study proved that current bioinformatics software tools and approaches can be used to successfully assemble and characterize a large proportion of the transcriptome of a complex eukaryotic organism. This approach can be used to characterise the gene catalog of a wide range of non-model organisms using only data derived from uHTS experiments.

Genomic and Transcriptomic Reference Assemblies and Analyses with Sequencing Datasets from Multiple Non-traditional Model Species

Download Genomic and Transcriptomic Reference Assemblies and Analyses with Sequencing Datasets from Multiple Non-traditional Model Species PDF Online Free

Author : Lisa Kristine Johnson
Publisher :
ISBN 13 : 9781658413824
Total Pages : pages
Book Rating : 4.4/5 (138 download)

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Book Synopsis Genomic and Transcriptomic Reference Assemblies and Analyses with Sequencing Datasets from Multiple Non-traditional Model Species by : Lisa Kristine Johnson

Download or read book Genomic and Transcriptomic Reference Assemblies and Analyses with Sequencing Datasets from Multiple Non-traditional Model Species written by Lisa Kristine Johnson and published by . This book was released on 2019 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: High-throughput nucleic acid "Next-Generation" sequencing (NGS) methods have revolutionized the biological sciences over the past decade by facilitating research and discoveries at the whole-genome level. However, generating high-quality genome and transcriptome references and navigating downstream analyses still remain challenging and computationally-intensive endeavors, especially for non-model species. This dissertation focused on automating bioinformatics methods for two different projects with multiple non-model species: the Marine Microbial Eukaryotic Transcriptome Sequencing Project (MMETSP) and differential expression analysis of gill epithelium from Fundulus North American killifish following salinity challenge. With these two projects, I sought to generate high quality de novo transcriptomes and genomes in a uniform and automated way. Three aims were addressed: how the re-analysis of old data with new tools affects the outcome of the reference assemblies, how to generate data and draft de novo assemblies for several high-quality reference genomes from non-model species in a cost-efficient manner, and how to generate high quality species-specific de novo transcriptomes and annotations using annotations from a closely-related model species reference. Furthermore, I used these de novo transcriptomes and annotations to examine gene expression responses of multiple species of Fundulus killifish to a common salinity challenge experiment.

Evolutionary Conservation Genetics

Author : Jacob Höglund
Publisher : Oxford University Press
ISBN 13 : 0191550264
Total Pages : pages
Book Rating : 4.1/5 (915 download)

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Book Synopsis Evolutionary Conservation Genetics by : Jacob Höglund

Download or read book Evolutionary Conservation Genetics written by Jacob Höglund and published by Oxford University Press. This book was released on 2009-03-19 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: Conservation genetics focuses on understanding the role and requirement of genetic variation for population persistence. However, considerable debate now surrounds the role of genetic factors (as opposed to non-genetic factors such as habitat destruction etc.) in population extinction, and a comprehensive synthesis is now timely. Can extinction be explained by habitat destruction alone or is lack of genetic variation a part of the explanation? The book thoroughly reviews the arguments for a role of genetics in the present biodiversity crisis. It describes the methods used to study genetic variation in endangered species and examines the influence of genetic variation in the extinction of species. To date, conservation genetics has predominantly utilized neutral genetic markers e.g. microsatellites. However, with the recent advances in molecular genetics and genomics it will soon be possible to study 'direct gene action', following the fate of genetic variation at the level of DNA, through expression, to proteins in order to determine how such phenotypes fare in populations of free living organisms. Evolutionary Conservation Genetics explores these exciting avenues of future research potential, integrating ecological quantitative genetics with the new genome science. It is now more important than ever that we ask relevant questions about the evolutionary fate of endangered populations throughout the globe and incorporate our knowledge of evolutionary processes and the distribution of genetic diversity into effective conservation planning and action.

Systems Biology

Author : Bernhard Palsson
Publisher : Cambridge University Press
ISBN 13 : 1107038855
Total Pages : 551 pages
Book Rating : 4.1/5 (7 download)

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Book Synopsis Systems Biology by : Bernhard Palsson

Download or read book Systems Biology written by Bernhard Palsson and published by Cambridge University Press. This book was released on 2015-01-26 with total page 551 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first comprehensive single-authored textbook on genome-scale models and the bottom-up approach to systems biology.

Plant Comparative Genomics

Author : Alejandro Pereira-Santana
Publisher : Springer Nature
ISBN 13 : 1071624296
Total Pages : 293 pages
Book Rating : 4.0/5 (716 download)

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Book Synopsis Plant Comparative Genomics by : Alejandro Pereira-Santana

Download or read book Plant Comparative Genomics written by Alejandro Pereira-Santana and published by Springer Nature. This book was released on 2022-07-11 with total page 293 pages. Available in PDF, EPUB and Kindle. Book excerpt: This detailed book presents recent methodologies for the task of inspecting the genomic world of plants, extracting valuable information, and presenting it in a readable way. With a focus on bioinformatics tools, the volume explores phylogenetics and evolution, Omics analysis, as well as experimental procedures for trait characterization. Written for the highly successful Methods in Molecular Biology series, chapters include the kind of vital expert implementation advice that will lead to successful results. Authoritative and practical, Plant Comparative Genomics serves as an ideal resource for researchers looking to implement comparative tools in order to explore their genomic data for their daily scientific work.

Encyclopedia of Bioinformatics and Computational Biology

Author :
Publisher : Elsevier
ISBN 13 : 0128114320
Total Pages : 3421 pages
Book Rating : 4.1/5 (281 download)

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Book Synopsis Encyclopedia of Bioinformatics and Computational Biology by :

Download or read book Encyclopedia of Bioinformatics and Computational Biology written by and published by Elsevier. This book was released on 2018-08-21 with total page 3421 pages. Available in PDF, EPUB and Kindle. Book excerpt: Encyclopedia of Bioinformatics and Computational Biology: ABC of Bioinformatics, Three Volume Set combines elements of computer science, information technology, mathematics, statistics and biotechnology, providing the methodology and in silico solutions to mine biological data and processes. The book covers Theory, Topics and Applications, with a special focus on Integrative –omics and Systems Biology. The theoretical, methodological underpinnings of BCB, including phylogeny are covered, as are more current areas of focus, such as translational bioinformatics, cheminformatics, and environmental informatics. Finally, Applications provide guidance for commonly asked questions. This major reference work spans basic and cutting-edge methodologies authored by leaders in the field, providing an invaluable resource for students, scientists, professionals in research institutes, and a broad swath of researchers in biotechnology and the biomedical and pharmaceutical industries. Brings together information from computer science, information technology, mathematics, statistics and biotechnology Written and reviewed by leading experts in the field, providing a unique and authoritative resource Focuses on the main theoretical and methodological concepts before expanding on specific topics and applications Includes interactive images, multimedia tools and crosslinking to further resources and databases

The Oil Palm Genome

Author : Maizura Ithnin
Publisher : Springer Nature
ISBN 13 : 3030225496
Total Pages : 165 pages
Book Rating : 4.0/5 (32 download)

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Book Synopsis The Oil Palm Genome by : Maizura Ithnin

Download or read book The Oil Palm Genome written by Maizura Ithnin and published by Springer Nature. This book was released on 2020-06-12 with total page 165 pages. Available in PDF, EPUB and Kindle. Book excerpt: This book compiles the fundamental advances resulting from of oil-palm genome and transcriptome sequencing, and describes the challenges faced and strategies applied in sequencing, assembling and annotating oil palm genome sequences. The availability of genome and transcriptome data has made the mining of a high number of new molecular markers useful for genetic diversity as well as marker-trait association studies and the book presents high-throughput genotyping platforms, which allow the detection of QTL regions associated with interesting oil palm traits such as oil unsaturation and yield components using classical genetic and association mapping approaches. Lastly, it also presents the discovery of major genes governing economically important traits of the oil palm. Covering the history of oil palm expansion, classical and molecular cytogenetics, improvements based on wild and advanced genetic materials, and the science of oil palm breeding, the book is a valuable resource for scientists involved in plant genetic research.