作者: 討人喜歡 時間: 2025-3-21 20:53 作者: nostrum 時間: 2025-3-22 03:01
Inferring Phylogenomic Relationship of Microbes Using Scalable Alignment-Free Methodses of bacteria and archaea, based on short, subsequences of length . (.-mers). We describe how this strategy can be extended to infer evolutionary relationships beyond a tree-like structure, to better capture both vertical and lateral signals of microbial evolution.作者: 烤架 時間: 2025-3-22 05:54 作者: Mingle 時間: 2025-3-22 10:04
1064-3745 in bacterial genomics and for less experienced researchers, including students and teachers, who could use a reference for approaching genomic analysis and genome data..978-1-0716-1101-2978-1-0716-1099-2Series ISSN 1064-3745 Series E-ISSN 1940-6029 作者: 剛開始 時間: 2025-3-22 12:56
https://doi.org/10.1007/978-3-531-92247-8sed on open-source software that might be handled also by non-bioinformaticians interested in transformation of sequencing data into reliable biological information. With the use of this method, we successfully closed six . genomes, while the assembly process was run just on a slightly improved desktop computer.作者: 暫時過來 時間: 2025-3-22 20:09
Fritz B?hle,G. Günter Vo?,Günther Wachtlerquencing outputs to match a wide range of applications from complete genome sequencing to metagenomics analysis. In this chapter, after explaining how to assemble a normalized pool of libraries for sequencing, we will describe the experimental steps required to run the pools on the NovaSeq 6000 platform.作者: 假裝是你 時間: 2025-3-22 23:57
Wolfgang Strengmann-Kuhn,Richard Hausered metagenomic assembly workflow including read quality filtering, assembly, contig/scaffold binning, and postassembly check for genome completeness and contamination. We also describe a case study to reconstruct near-complete microbial genomes from metagenomes using our workflow.作者: 狼群 時間: 2025-3-23 05:05
International vergleichende Armutsforschungon taxonomic and functional features of bacterial communities inhabiting the lungs of cystic fibrosis patients. Models are built in the R environment by using different freely available machine learning algorithms.作者: foreign 時間: 2025-3-23 08:18 作者: Cubicle 時間: 2025-3-23 13:19 作者: fixed-joint 時間: 2025-3-23 14:58 作者: Notify 時間: 2025-3-23 18:31
1064-3745 expertsThis completely revised edition explores novel discoveries in bacterial genomic research, with a focus on technical and computational improvements as well as methods used for bacterial pangenome analysis, which relies on microbiome studies and metagenomic data. Beginning with up-to-date sequ作者: 小步舞 時間: 2025-3-23 23:51 作者: 歌劇等 時間: 2025-3-24 05:22
Fritz B?hle,G. Günter Vo?,Günther Wachtlercan be computationally challenging. Our program . quickly computes accurate pairwise distances between up to thousands of bacterial genomes. Working under the UNIX command line, we show how . can be used to transform genomes to phylogenies with support values ready to be printed or integrated into documents.作者: 解決 時間: 2025-3-24 09:50
Inferring Core Genome Phylogenies for Bacteriaenomic data to final phylogenetic analyses based on 107 conserved single copy genes. This approach can be used to perform phylogenetic reconstructions with high resolution on strain level or across taxa spanning different clades of the bacterial tree of life.作者: BUDGE 時間: 2025-3-24 11:58
Fast Phylogeny Reconstruction from Genomes of Closely Related Microbescan be computationally challenging. Our program . quickly computes accurate pairwise distances between up to thousands of bacterial genomes. Working under the UNIX command line, we show how . can be used to transform genomes to phylogenies with support values ready to be printed or integrated into documents.作者: 弄污 時間: 2025-3-24 17:34 作者: IRS 時間: 2025-3-24 20:43
The Illumina Sequencing Protocol and the NovaSeq 6000 Systemquencing outputs to match a wide range of applications from complete genome sequencing to metagenomics analysis. In this chapter, after explaining how to assemble a normalized pool of libraries for sequencing, we will describe the experimental steps required to run the pools on the NovaSeq 6000 platform.作者: 偶然 時間: 2025-3-25 02:31
Metagenomic Assembly: Reconstructing Genomes from Metagenomesed metagenomic assembly workflow including read quality filtering, assembly, contig/scaffold binning, and postassembly check for genome completeness and contamination. We also describe a case study to reconstruct near-complete microbial genomes from metagenomes using our workflow.作者: Irrigate 時間: 2025-3-25 05:31
Host Trait Prediction from High-Resolution Microbial Featureson taxonomic and functional features of bacterial communities inhabiting the lungs of cystic fibrosis patients. Models are built in the R environment by using different freely available machine learning algorithms.作者: Kinetic 時間: 2025-3-25 07:40
Phylogenetic Methods for Genome-Wide Association Studies in Bacterias to use a phylogenetic approach, which is based on long-standing methodology for the evolutionary analysis of bacterial genomic data. Here we present both the theoretical and practical aspects involved in the use of phylogenetic methods for bacterial genome-wide association studies.作者: Nerve-Block 時間: 2025-3-25 12:21
International vergleichende Armutsforschungo identify core sets of genes in the context of a pangenome. The first section will focus on the methods to provide metagenomic genes with accurate annotations. The second part will describe how to combine the gene catalog information with metagenome-assembled genomes and how to use both to build and investigate a pangenome.作者: 爭議的蘋果 時間: 2025-3-25 16:37
Wolfgang Strengmann-Kuhn,Richard Hauseration is obtained, scientists would be able to highlight the relative abundance of ARGs in the metagenome analyzed and be able to understand how antibiotic resistance mechanisms evolve in microbial communities.作者: PANIC 時間: 2025-3-25 21:52
International vergleichende Armutsforschungresented. MAISEN is a free, web-based tool designed to accelerate manual annotation, by providing the user with simple interface and precomputed alignments for each predicted feature. It was designed to be available for every scientist, regardless of their bioinformatic proficiency.作者: 文件夾 時間: 2025-3-26 00:20 作者: crutch 時間: 2025-3-26 07:50 作者: ectropion 時間: 2025-3-26 10:50
Simple, Reliable, and Time-Efficient Manual Annotation of Bacterial Genomes with MAISENresented. MAISEN is a free, web-based tool designed to accelerate manual annotation, by providing the user with simple interface and precomputed alignments for each predicted feature. It was designed to be available for every scientist, regardless of their bioinformatic proficiency.作者: 摘要記錄 時間: 2025-3-26 14:46 作者: foliage 時間: 2025-3-26 18:01
Book 2021Latest editionwell as methods used for bacterial pangenome analysis, which relies on microbiome studies and metagenomic data. Beginning with up-to-date sequencing methods, the book continues with sections covering methods for deep phylogenetic analysis, the role of metagenomic data in understanding the genomics o作者: 閑逛 時間: 2025-3-27 00:13
PacBio-Based Protocol for Bacterial Genome Assemblyelopment of sensitive species-specific tools for detection and identification of the pathogens. In this view, Pacific Biosciences technology seems highly tempting taking into consideration over 10,000?bp length of the generated reads. In this work, we describe a bacterial genome assembly pipeline ba作者: cliche 時間: 2025-3-27 01:06
The Illumina Sequencing Protocol and the NovaSeq 6000 Systeme typical Illumina sequencing workflow based on library preparation, cluster generation by in situ amplification, and sequencing by synthesis. Flexibility is one of the major features of the NovaSeq 6000. Several types of sequencing kits coupled with dual flow cell mode enable high scalability of se作者: 同來核對 時間: 2025-3-27 06:26 作者: 全部逛商店 時間: 2025-3-27 12:35
Inferring Core Genome Phylogenies for Bacteriaed on more than a single or few marker genes have become feasible. In this method protocol, we describe the complete bioinformatic workflow from raw genomic data to final phylogenetic analyses based on 107 conserved single copy genes. This approach can be used to perform phylogenetic reconstructions作者: Working-Memory 時間: 2025-3-27 16:06 作者: 手術(shù)刀 時間: 2025-3-27 20:59
Fast Phylogeny Reconstruction from Genomes of Closely Related Microbesge in technology is leading to the rapid accumulation of large samples of closely related genome sequences. Summarizing such samples into phylogenies can be computationally challenging. Our program . quickly computes accurate pairwise distances between up to thousands of bacterial genomes. Working u作者: Horizon 時間: 2025-3-27 23:50
Comparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Studyassembled bacterial?genomes. It rapidly became clear that digging out useful biological information from such a huge amount of data presents a considerable challenge. In this chapter we share our experience with utilization?of several handy open source comparative genomic tools. All of them were app作者: BUCK 時間: 2025-3-28 04:43
Accurate Annotation of Microbial Metagenomic Genes and Identification of Core Sets information has the potential to widen our understanding of the functioning of microbial communities and their roles in the environment. A fundamental step in this process is the functional and taxonomic profiling of the metagenomes, through an accurate gene annotation. This gene-level information 作者: V洗浴 時間: 2025-3-28 06:57
Metagenomic Assembly: Reconstructing Genomes from Metagenomesional capacity of microorganisms. The rapid development of sequencing technology and novel assembly algorithms have made it possible to reliably reconstruct hundreds to thousands of microbial genomes from raw sequencing reads through metagenomic assembly. In this chapter, we introduce a routinely us作者: 擁護 時間: 2025-3-28 11:46
Genome Recovery, Functional Profiling, and Taxonomic Classification from Metagenomesarches without a specialistic bioinformatic background. In this chapter we review all the steps that lead from raw reads to a collection of quality-controlled, functionally annotated bacterial genomes and propose a working protocol using state-of-the-art, open source software tools.作者: constellation 時間: 2025-3-28 17:00 作者: 合乎習(xí)俗 時間: 2025-3-28 21:04
Host Trait Prediction from High-Resolution Microbial Featuresformatics and/or statistics. Profiling bacterial communities using shotgun metagenomics often leads to the generation of a large amount of data that cannot be used directly for training a model. In this chapter we provide a detailed description of how to build a working machine learning model based 作者: Confess 時間: 2025-3-29 01:15 作者: 新鮮 時間: 2025-3-29 03:17
Simple, Reliable, and Time-Efficient Manual Annotation of Bacterial Genomes with MAISENic curation and storage. A huge number of available DNA sequences (including genomes and metagenomes) resulted in the development of various tools for sequence annotation. While much effort has been invested into the development of automatic annotation pipelines, manual curation of their results is 作者: choleretic 時間: 2025-3-29 10:33
Genome Recovery, Functional Profiling, and Taxonomic Classification from Metagenomesarches without a specialistic bioinformatic background. In this chapter we review all the steps that lead from raw reads to a collection of quality-controlled, functionally annotated bacterial genomes and propose a working protocol using state-of-the-art, open source software tools.作者: somnambulism 時間: 2025-3-29 12:30 作者: 脾氣暴躁的人 時間: 2025-3-29 15:53
Wolfgang Strengmann-Kuhn,Richard Hauserarches without a specialistic bioinformatic background. In this chapter we review all the steps that lead from raw reads to a collection of quality-controlled, functionally annotated bacterial genomes and propose a working protocol using state-of-the-art, open source software tools.作者: 群島 時間: 2025-3-29 23:35
Alessio Mengoni,Giovanni Bacci,Marco FondiIncludes cutting-edge techniques.Provides step-by-step detail essential for reproducible results.Contains key implementation advice from the experts作者: faddish 時間: 2025-3-30 01:32 作者: Exuberance 時間: 2025-3-30 07:51
https://doi.org/10.1007/978-1-0716-1099-2Sequencing technologies; Cultured isolates; Genome-to-phenome inference; Prokaryotic genomics; Metagenom作者: 兇兆 時間: 2025-3-30 08:54 作者: 礦石 時間: 2025-3-30 15:02
https://doi.org/10.1007/978-3-531-92247-8elopment of sensitive species-specific tools for detection and identification of the pathogens. In this view, Pacific Biosciences technology seems highly tempting taking into consideration over 10,000?bp length of the generated reads. In this work, we describe a bacterial genome assembly pipeline ba作者: 衰弱的心 時間: 2025-3-30 18:31
Fritz B?hle,G. Günter Vo?,Günther Wachtlere typical Illumina sequencing workflow based on library preparation, cluster generation by in situ amplification, and sequencing by synthesis. Flexibility is one of the major features of the NovaSeq 6000. Several types of sequencing kits coupled with dual flow cell mode enable high scalability of se作者: 難聽的聲音 時間: 2025-3-31 00:12
Fritz B?hle,G. Günter Vo?,Günther Wachtlers critical for environmental adaptation, particularly considering a theoretically unlimited number of niches on the earth for microorganisms. Comparative genomics can reveal a co-occurrence pattern between a subset of accessory genes (or variations in core genes) and an adaptation trait, while compa
