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Molecular Modeling of Nucleic Acid Structure: Energy and Sampling

Abstract Table of Contents Figures Literature Cited Abstract An overview of computer simulation techniques as applied to nucleic acid systems is presented. This unit discusses methods used to treat energy and to sample representative confi

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Molecular Modeling of Nucleic Acid Structure

Abstract Table of Contents Figures Literature Cited Abstract This unit is the first in a series of four units covering the analysis of nucleic acid structure by molecular modeling. The unit provides an overview of the computer simulation o

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RNA Structure Analysis of Viruses Using SHAPE

Abstract Table of Contents Materials Literature Cited Abstract Selective 2? hydroxyl acylation analyzed by primer extension (SHAPE) provides a means to investigate RNA structure with better resolution and higher throughput than has been po

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Identification of Mutations in Zebrafish Using Next‐Generation Sequencing

Abstract Table of Contents Materials Figures Literature Cited Abstract Whole?genome sequencing (WGS) has been used in many invertebrate model organisms as an efficient tool for mapping and identification

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Analysis and Annotation of Whole‐Genome or Whole‐Exome Sequencing–Derived Variants for Clinical Diagnosis

Abstract Table of Contents Figures Literature Cited Abstract Over the last several years, next?generation sequencing (NGS) has transformed genomic research through substantial advances in technology and reduction in the cost of sequencing,

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Genome‐Scale Sequencing to Identify Genes Involved in Mendelian Disorders

Abstract Table of Contents Figures Literature Cited Abstract The analysis of genome?scale sequence data can be defined as the interrogation of a complete set of genetic instructions in a search for individual loci that produce or contribut

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Analyzing Copy Number Variation Using SNP Array Data: Protocols for Calling CNV and Association Tests

Abstract Table of Contents Materials Figures Literature Cited Abstract High?density SNP genotyping technology provides a low?cost, effective tool for conducting Genome Wide Association (GWA) studies. The

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LipidXplorer: Software for Quantitative Shotgun Lipidomics Compatible with Multiple Mass Spectrometry Platforms

Abstract Table of Contents Figures Literature Cited Abstract LipidXplorer is an open?source software kit that supports the identification and quantification of molecular species of any lipid class detected by shotgun experiments performed

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From FastQ Data to High‐Confidence Variant Calls: The Genome Analysis Toolkit Best Practices Pipeline

Abstract Table of Contents Figures Literature Cited Abstract This unit describes how to use BWA and the Genome Analysis Toolkit (GATK) to map genome sequencing data to a reference and produce high?quality variant calls that can be used in

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Cloud Computing with iPlant Atmosphere

Abstract Table of Contents Figures Literature Cited Abstract Cloud Computing refers to distributed computing platforms that use virtualization software to provide easy access to physical computing infrastructure and data storage, typically

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Selecting the Right Similarity‐Scoring Matrix

Abstract Table of Contents Figures Literature Cited Abstract Protein sequence similarity searching programs like BLASTP, SSEARCH, and FASTA use scoring matrices that are designed to identify distant evolutionary relationships (BLOSUM62 for

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RAMPAGE: Promoter Activity Profiling by Paired‐End Sequencing of 5′‐Complete cDNAs

Abstract Table of Contents Materials Figures Literature Cited Abstract RNA annotation and mapping of promoters for analysis of gene expression (RAMPAGE) is a method that harnesses highly specific sequenci

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Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation

Abstract Table of Contents Figures Literature Cited Abstract This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete a

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PepArML: A Meta‐Search Peptide Identification Platform for Tandem Mass Spectra

Abstract Table of Contents Materials Figures Literature Cited Abstract The PepArML meta?search peptide identification platform for tandem mass spectra provides a unified search interface to seven search e

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STRAP PTM: Software Tool for Rapid Annotation and Differential Comparison of Protein Post‐Translational Modifications

Abstract Table of Contents Figures Literature Cited Abstract The identification of protein post?translational modifications (PTMs) is an increasingly important component of proteomics and biomarker discovery, but very few tools exist for p

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Using SOAPaligner for Short Reads Alignment

Abstract Table of Contents Literature Cited Abstract This unit shows how to use the SOAPaligner package to align short reads to reference. The use of the two most common versions of SOAPaligner, SOAP2 and SOAP3?dp, will be described in detail. The unit also includes a proto

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mtDNA Variation and Analysis Using Mitomap and Mitomaster

Abstract Table of Contents Figures Literature Cited Abstract The Mitomap database of human mitochondrial DNA (mtDNA) information has been an important compilation of mtDNA variation for researchers, clinicians, and genetic counselors for t

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研究生如何提高工作效率

本文主要根据《科学》年度最佳故事12月16日的Improve Your Productivity in Graduate School整理,请参看原文。研究生是时间长任务重的人生阶段,尽管每个人的理解可能不同,但如何把研究生阶段经营好,确实可能会影响个人的科研生命。作者根据自己的研究生生活经验,给大家提供一些如何提高研究效率的建议。因为作者是美国的科学类研究生,和国内的情况有所不同,不同专业也不一样,但这个文章仍有参考价值,对希望 ...

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SCI论文写作

从开始准备到SCI论文投稿点此查看全文2、如何在科技论文中使用时态http://www.biomart.cn/news/10/80471.htm3、中国作者英文科技论文中常见语言问题在中国作者的英文论文中,经常会有很多不符合英、美英语习惯的表述,造成审稿人或期刊编辑误解文章所要表达的意思,从而影响了学术交流甚至有文章因此被拒稿。点此查看全文4、如何制作科技论文中的Figureshttp://www.biomart.cn ...

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什么是期刊杂志的索引(Index)

任何一本期刊杂志,想要提高其权威度,第一前提便是它的受众影响范围。索引及摘要服务,就是这样一个工具,用来导引研究人员至其相关的领域的文章,并最终促进信息的广泛传播。当一本期刊被推出后,如果其能保持一个按时出版的记录,且每期都有实实在在的内容,那么该杂志就会被考虑纳入索引以及摘要服务中。一旦具备了稳定的文章数量、质量、及固定的出版进度,那么杂志社就是时候接触一个或几个提供索引摘要服务的供应商了。虽然每个学科可能有 ...

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