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CheckM:微生物基因组组装/metagenome基因组重构完整度和杂合度评估

标题:

CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes

摘要:

Large-scale recovery of genomes from isolates, single cells, and metagenomic data has been made possible by advances in computational methods and substantial reductions in sequencing costs. While this increasing breadth of draft genomes is providing key information regarding the […]

Minute.of.Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences

期刊:Nature Reviews Microbiology

IF:23.317

链接:http://www.nature.com/nrmicro/journal/v12/n9/abs/nrmicro3330.html

简要:

Small subunit ribosomal RNA gene,亦即熟知的细菌(Bac.)与古菌(Arc.)这些原核生物中的16S rRNA。对16S rRNA的研究以及在公开提供的数据库中的序列数都迅速增长,序列条目已经超过400万。然而,对于细菌和古菌的分类和命名并没有统一的框架标准。

在这篇分析性文章中,研究人员通过对16S rRNA序列数据库中的大量数据进行分析和分类命名术语汇总,提出了基于16s rRNA序列identities对Bac.和Arc.在高阶分类水平的合理分类边界(Rational taxonomic boundaries),包括了:细菌与古菌在高阶分类水平(High taxa)上的合理的分类界域,更新了关于球细菌与古菌的种类和数量普查结果,以及阐述了可通用于可培养的和不可培养的微生物的在高阶分类水平的稳定层次分类方法(Stable hierarchical classification of high taxa)的原理。。同时,对数据的分析发现,只有近乎全长16S rRNA 的数据才能提供物种分类多样性或差异的准确评估。另外,对现有数据的分析发现当前对于环境样品的研究研究大多数止步于高阶的分类水平。

概要记录:

1、 It is remarkable that, although nearly 1.3 million eukaryotic species have […]

RNA-seq 序列错误纠正评估

文章:

Optimizing error correction of RNAseq reads

摘要:

Motivation:The correction of sequencing errors contained in Illumina reads derived from genomic DNA is a common pre-processing step in many de novo genome assembly pipelines, and has been shown to improved the quality of resultant assemblies. In contrast, the correction of errors in transcriptome sequence data is […]

Sam/bam 版本 1.5 支持基因组重头数据拼装

文章:

SAM/BAM format v1.5 extensions for de novo assemblies

摘要:

The plain text Sequence Alignment/Map (SAM) file format and its companion binary form (BAM) are a generic alignment format for storing read alignments against reference sequences (and unmapped reads) together with structured meta-data (Li et al., 2009). Driven by the needs of the 1000 Genomes […]

基因表达水平高低的影响因素分析

细胞表达一个基因,即将基因转录成RNA,,并翻译成蛋白的效率是不同的。除与基因本身有关外,表达水平的高低也与细胞中的各种分子机器启动基因表达的强度有关。如启动子就是RNA转录的必需因子,而RBS也是对该过程有重要影响的因素。在过去,很多科学家已经从微生物中鉴定出各种不同强度的启动子,RBS等调控元件,并利用这些元件调控基因的表达水平。但是在实践中,利用这些调控元件表达相关基因的活性与预测的结果相差甚远。这两篇文章向大家介绍影响原核生物基因表达水平高低的主要调控元件。在此基础上,BIOFAB的工作人员设计了BCD结构,这个元件不干扰下游在DNA的启动子和RBS序列,且与搭配的基因无关,能够更严格的控制基因的表达,使基因表达水平与预测水平之间的符合度达到93%。这项研究对精确调控基因表达有重要的作用。

Related paper: Mutalik, V. K., et al. (2013). “Quantitative estimation of activity and quality for collections of functional genetic elements.” Nature methods. Mutalik, V. K., et al. (2013). “Precise and reliable gene expression via standard transcription and translation initiation elements.” Nature methods 10(4): 354-360.

Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds

Oil palm genome sequence reveals divergence of interfertile species in Old and New worlds

links: doi:10.1038/nature12309 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12309.html Genome Sequence and assembly

The assembly of E. guineensis (AVROS, pisifera fruit form) genome P5-build was constructed from sequences from a total of 148 linker libraries and 81 fragment libraries (Roche/454). Reads were generated from genomic DNA fragment […]

Development of microsatellite markers by transcriptome sequencing in two species of Amorphophallus (Araceae)

Development of microsatellite markers by transcriptome sequencing in two species of Amorphophallus (Araceae)

links: BMC Genomics 2013, 14:490 doi:10.1186/1471-2164-14-490. http://www.biomedcentral.com/1471-2164/14/490/abstract Abstract

Background

Amorphophallus is a genus of perennial plants widely distributed in the tropics or subtropics of West Africa and South Asia. Its corms contain a high level of water-soluble glucomannan; therefore, it has long […]

Coelacanth genomes reveal signatures for evolutionary transition from water to land

Coelacanth genomes reveal signatures for evolutionary transition from water to land

links: http://genome.cshlp.org/content/early/2013/07/19/gr.158105.113.abstract

Assembling the coelacanth genome

First, we constructed the reference coelacanth draft genome from one of the Tanzanian specimens (TCC041-004, gender unknown; Nikaido et al. 2011), which was recovered from the body cavity of its mother (coelacanths give birth to fully formed offspring; […]

The Norway spruce genome sequence and conifer genome evolution

The Norway spruce genome sequence and conifer genome evolution

文章地址: Nature http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12211.html

Supplementary Material

Haploid whole genome shotgun sequencing and assembly

Seeds from the P. abies clone Z4006 were stored at -20° C at Skogforsk Sävar, then soaked in water overnight, and manually dissected under a microscope to free the haploid megagametophyte tissue. Total DNA […]

NGS++: a library for rapid prototyping of epigenomics software tools

NGS++: a library for rapid prototyping of epigenomics software tools

文章地址:NGS++: a library for rapid prototyping of epigenomics software tools

Abstract Motivation: The development of computational tools to enable testing and analysis of high-throughput–sequencing data is essential to modern genomics research. However, although multiple frameworks have been developed to facilitate access to these tools, comparatively […]