Abstract：
:Long-read sequencing technologies have become increasingly popular due to their strengths in resolving complex genomic regions. As a leading model organism with small genome size and great biotechnological importance, the budding yeast Saccharomyces cerevisiae has many isolates currently being sequenced with long reads. However, analyzing long-read sequencing data to produce high-quality genome assembly and annotation remains challenging. Here, we present a modular computational framework named long-read sequencing data analysis for yeasts (LRSDAY), the first one-stop solution that streamlines this process. Starting from the raw sequencing reads, LRSDAY can produce chromosome-level genome assembly and comprehensive genome annotation in a highly automated manner with minimal manual intervention, which is not possible using any alternative tool available to date. The annotated genomic features include centromeres, protein-coding genes, tRNAs, transposable elements (TEs), and telomere-associated elements. Although tailored for S. cerevisiae, we designed LRSDAY to be highly modular and customizable, making it adaptable to virtually any eukaryotic organism. When applying LRSDAY to an S. cerevisiae strain, it takes ∼41 h to generate a complete and well-annotated genome from ∼100× Pacific Biosciences (PacBio) running the basic workflow with four threads. Basic experience working within the Linux command-line environment is recommended for carrying out the analysis using LRSDAY.
journal_name
Nat Protocjournal_title
Nature protocolsauthors
Yue JX,Liti Gdoi
10.1038/nprot.2018.025subject
Has Abstractpub_date
2018-06-01 00:00:00pages
1213-1231issue
6eissn
1754-2189issn
1750-2799pii
nprot.2018.025journal_volume
13pub_type
杂志文章相关文献
Nature Protocols文献大全abstract：:Post-translational modifications alter protein structure, affecting activity, stability, localization and/or binding partners. Antibodies that specifically recognize post-translationally modified proteins have a number of uses including immunocytochemistry and immunoprecipitation of the modified protein to purify prot...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2014.017
更新日期：2014-02-01 00:00:00
abstract：:At present, several assays that use radioisotope labeling to quantify the degradation of long-lived proteins have been developed to measure autophagic flux. Here, we describe a nonradioactive pulse-chase protocol using L-azidohomoalanine (AHA) labeling to quantify long-lived protein degradation during autophagy. AHA i...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2016.160
更新日期：2017-12-01 00:00:00
abstract：:New technologies have recently enabled saturation mutagenesis and functional analysis of nearly all possible variants of regulatory elements or proteins of interest in single experiments. Here we discuss the past, present, and future of such multiplexed (functional) assays for variant effects (MAVEs). MAVEs provide de...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2016.135
更新日期：2016-10-01 00:00:00
abstract：:Precise identification of sites of RNA modification is key to studying the functional role of such modifications in the regulation of gene expression and for elucidating relevance to diverse physiological processes. tRNA reduction and cleavage sequencing (TRAC-Seq) is a chemically based approach for the unbiased globa...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/s41596-019-0226-7
更新日期：2019-11-01 00:00:00
abstract：:Genetically encoded fluorescent proteins (FPs) are highly utilized in cell biology research to study proteins of interest or signal processes using biosensors. To perform well in specific applications, these FPs require a multitude of tailored properties. It is for this reason that they need to be optimized by using m...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/s41596-019-0250-7
更新日期：2020-02-01 00:00:00
abstract：:The transmembrane (TM) anchors of cell surface proteins have been one of the 'blind spots' in structural biology because they are generally very hydrophobic, sometimes dynamic, and thus difficult targets for structural characterization. A plethora of examples show these membrane anchors are not merely anchors but can ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/s41596-019-0188-9
更新日期：2019-08-01 00:00:00
abstract：:In the version of this protocol originally published, the caption for Fig. 3 was erroneously placed with Fig. 4, and that for Fig. 4 was placed with Fig. 3. This error has been corrected in the HTML and PDF versions of the paper. ...
journal_title：Nature protocols
pub_type： 已发布勘误
doi：10.1038/s41596-018-0079-5
更新日期：2019-07-01 00:00:00
abstract：:Although lung transplant is a life-saving therapy for some patients, primary graft dysfunction (PGD) is a leading cause of mortality and morbidity soon after a transplant. Ischemia reperfusion injury is known to be one of the most critical factors in PGD development. PGD is by definition an acute lung injury syndrome ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/s41596-018-0019-4
更新日期：2018-08-01 00:00:00
abstract：:The Golgi apparatus undergoes extensive disassembly during mitosis and reassembly in post-mitotic daughter cells. This process has been mimicked in vitro by treating Golgi membranes with mitotic and interphase cytosol. To determine the minimal machinery that controls the morphological change, we have developed a defin...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2010.38
更新日期：2010-04-01 00:00:00
abstract：:This protocol outlines the carboxyfluorescein diacetate succinimidyl ester (CFSE) method for following the proliferation of human lymphocytes in vitro and mouse lymphocytes both in vitro and in vivo. The method relies on the ability of CFSE to covalently label long-lived intracellular molecules with the highly fluores...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2007.296
更新日期：2007-01-01 00:00:00
abstract：:This protocol measures externalization of aminophospholipids (APLs) to the outside of the plasma membrane using mass spectrometry (MS). APL externalization occurs in numerous events, and it is relevant for transplant medicine, immunity and cancer. In this protocol, externalized APLs are chemically modified by using a ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2013.163
更新日期：2014-01-01 00:00:00
abstract：:This protocol explains how to discover functional signals in genomic sequences by detecting over- or under-represented oligonucleotides (words) or spaced pairs thereof (dyads) with the Regulatory Sequence Analysis Tools (http://rsat.ulb.ac.be/rsat/). Two typical applications are presented: (i) predicting transcription...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2008.98
更新日期：2008-01-01 00:00:00
abstract：:Gram-negative and Gram-positive bacteria release a variety of membrane vesicles through different formation routes. Knowledge of the structure, molecular cargo and function of bacterial extracellular vesicles (BEVs) is primarily obtained from bacteria cultured in laboratory conditions. BEVs in human body fluids have b...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/s41596-019-0236-5
更新日期：2020-01-01 00:00:00
abstract：:The bimolecular fluorescence complementation (BiFC) assay is a powerful tool for visualizing and identifying protein interactions in living cells. This assay is based on the principle of protein-fragment complementation, using two nonfluorescent fragments derived from fluorescent proteins. When two fragments are broug...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2008.16
更新日期：2008-01-01 00:00:00
abstract：:The adeno-associated virus (AAV) is one of the most promising viral vectors for human gene therapy. As with any potential therapeutic system, a thorough understanding of it at the in vitro and in vivo levels is required. Over the years, numerous methods have been developed to better characterize AAV vectors. These met...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2006.207
更新日期：2006-01-01 00:00:00
abstract：:Cell proliferation may be measured in vivo by quantifying DNA synthesis with isotopically labeled deoxyribonucleotide precursors. Deuterium-labeled glucose is one such precursor which, because it achieves high levels of enrichment for a short period, is well suited to the study of rapidly dividing cells, in contrast t...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2009.117
更新日期：2009-01-01 00:00:00
abstract：:High-throughput sequencing of the variable domains of immune receptors (antibodies and T cell receptors (TCRs)) is of key importance in the understanding of adaptive immune responses in health and disease. However, the sequencing of both immune receptor chains (VH+VL or TCRβ/δ+TCRα/γ) at the single-cell level for typi...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2016.024
更新日期：2016-03-01 00:00:00
abstract：:Rapid evaluation of microbial cell-surface carbohydrates is essential to understanding the mechanisms by which bacteria use glycans to establish pathogenic or symbiotic relationships. Microbial glycan analysis is complicated both by the vast diversity of possible carbohydrate structures and by their dynamic nature. Ba...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2006.76
更新日期：2006-01-01 00:00:00
abstract：:Apoptosis plays a pivotal role in the regulation of cell turnover, and a defect or an excess of apoptosis has been implicated in several human diseases. Apoptosis is activated from an extracellular death signal, or from an internal pathway starting from the endoplasmatic reticulum or the mitochondria. To investigate t...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2007.397
更新日期：2007-01-01 00:00:00
abstract：:Hydroxyl radical footprinting has been widely used for studying the structure of DNA and DNA-protein complexes. The high reactivity and lack of base specificity of the hydroxyl radical makes it an excellent probe for high-resolution footprinting of DNA-protein complexes; this technique can provide structural detail th...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2008.72
更新日期：2008-01-01 00:00:00
abstract：:Realizing the potential of human embryonic stem cells (hESCs) in research and commercial applications requires generic protocols for culture, expansion and genetic modification that function between multiple lines. Here we describe a feeder-free hESC culture protocol that was tested in 13 independent hESC lines derive...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2008.140
更新日期：2008-01-01 00:00:00
abstract：:Collagen-mimetic peptides and lipopeptides are widely used as substrates for matrix degrading enzymes, as new biomaterials for tissue engineering, as drug delivery systems and so on. However, the preparation and subsequent purification of these peptides and their fatty-acid conjugates are really challenging. Herein, w...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2009.195
更新日期：2010-01-01 00:00:00
abstract：:Improvement of cellular uptake and cellular localization is still one of the main obstacles to the development of antisense-antigene therapeutics, including peptide nucleic acid (PNA). Cell-penetrating peptides (CPPs) such as Tat peptide and polyarginine have been widely used to improve the cellular uptake of PNA and ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2006.92
更新日期：2006-01-01 00:00:00
abstract：:The lung epithelium is derived from the endodermal germ layer, which undergoes a complex series of endoderm-mesoderm-mediated signaling events to generate the final arborized network of conducting airways (bronchi, bronchioles) and gas-exchanging units (alveoli). These stages include endoderm induction, anterior-poste...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/s41596-018-0104-8
更新日期：2019-02-01 00:00:00
abstract：:High throughput microarray transcription analyses provide us with the expression profiles for large amounts of plant genes. However, their tissue and cellular resolution is limited. Thus, for detailed functional analysis, it is still necessary to examine the expression pattern of selected candidate genes at a cellular...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2006.333
更新日期：2006-01-01 00:00:00
abstract：:Multiplex-fluorescence in situ hybridization (M-FISH) was initially developed to stain human chromosomes--the 22 autosomes and X and Y sex chromosomes--with uniquely distinctive colors to facilitate karyotyping. The characteristic spectral signatures of all different combinations of fluorochromes are determined by mul...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2006.160
更新日期：2006-01-01 00:00:00
abstract：:Here, we provide comprehensive, highly efficient protocols for Agrobacterium tumefaciens-mediated transformation of a wide range of rice genotypes. Methods that use either immature embryos (japonica and indica rice) or calli (japonica cultivars and the indica cultivar, Kasalath) as a starting material for inoculation ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2008.46
更新日期：2008-01-01 00:00:00
abstract：:Protein ubiquitination is a versatile protein modification that regulates virtually all cellular processes. This versatility originates from polyubiquitin chains, which can be linked in eight distinct ways. The combinatorial complexity of eight linkage types in homotypic (one chain type per polymer) and heterotypic (m...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2015.018
更新日期：2015-02-01 00:00:00
abstract：:Postembryonic development is an important process of organismal maturation after embryonic growth. Despite key progress in recent years in understanding embryonic development via fluorescence time-lapse microscopy, comparatively less live-cell imaging of postembryonic development has been done. Here we describe a prot...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/nprot.2012.128
更新日期：2012-12-01 00:00:00
abstract：:Several noncanonical initial nucleotides (NCINs) have been found to cap RNAs and possibly regulate RNA stability, transcription and translation. NAD+ is one of the NCINs that has recently been discovered to cap RNAs in a wide range of species. Identification of the NAD+-capped RNAs (NAD-RNAs) could help to unveil the ...
journal_title：Nature protocols
pub_type： 杂志文章
doi：10.1038/s41596-020-0363-z
更新日期：2020-09-01 00:00:00
