Current protocols in bioinformatics最新文献_第8页

Using pLink to Analyze Cross-Linked Peptides 使用pLink分析交联肽

Current protocols in bioinformatics Pub Date : 2018-02-15 DOI: 10.1002/0471250953.bi0821s49

Sheng-Bo Fan, Jia-Ming Meng, Shan Lu, Kun Zhang, Hao Yang, Hao Chi, Rui-Xiang Sun, Meng-Qiu Dong, Si-Min He

{"title":"Using pLink to Analyze Cross-Linked Peptides","authors":"Sheng-Bo Fan, Jia-Ming Meng, Shan Lu, Kun Zhang, Hao Yang, Hao Chi, Rui-Xiang Sun, Meng-Qiu Dong, Si-Min He","doi":"10.1002/0471250953.bi0821s49","DOIUrl":"10.1002/0471250953.bi0821s49","url":null,"abstract":"pLink is a search engine for high-throughput identification of cross-linked peptides from their tandem mass spectra, which is the data-analysis step in chemical cross-linking of proteins coupled with mass spectrometry analysis. pLink has accumulated more than 200 registered users from all over the world since its first release in 2012. After 2 years of continual development, a new version of pLink has been released, which is at least 40 times faster, more versatile, and more user-friendly. Also, the function of the new pLink has been expanded to identifying endogenous protein cross-linking sites such as disulfide bonds and SUMO (Small Ubiquitin-like MOdifier) modification sites. Integrated into the new version are two accessory tools: pLabel, to annotate spectra of cross-linked peptides for visual inspection and publication, and pConfig, to assist users in setting up search parameters. Here, we provide detailed guidance on running a database search for identification of protein cross-links using the 2014 version of pLink. © 2015 by John Wiley & Sons, Inc.","PeriodicalId":10958,"journal":{"name":"Current protocols in bioinformatics","volume":"49 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/0471250953.bi0821s49","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32997649","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 30

Investigating Protein Structure and Evolution with SCOP2 利用SCOP2研究蛋白质结构和进化

Current protocols in bioinformatics Pub Date : 2018-02-15 DOI: 10.1002/0471250953.bi0126s49

Antonina Andreeva, Dave Howorth, Cyrus Chothia, Eugene Kulesha, Alexey G. Murzin

引用次数: 19

Expression Data Analysis with Reactome Reactome表达数据分析

Current protocols in bioinformatics Pub Date : 2018-02-15 DOI: 10.1002/0471250953.bi0820s49

Steve Jupe, Antonio Fabregat, Henning Hermjakob

引用次数: 16

Using REDItools to Detect RNA Editing Events in NGS Datasets 使用redittools检测NGS数据集中的RNA编辑事件

Current protocols in bioinformatics Pub Date : 2018-02-15 DOI: 10.1002/0471250953.bi1212s49

Ernesto Picardi, Anna Maria D'Erchia, Antonio Montalvo, Graziano Pesole

{"title":"Using REDItools to Detect RNA Editing Events in NGS Datasets","authors":"Ernesto Picardi, Anna Maria D'Erchia, Antonio Montalvo, Graziano Pesole","doi":"10.1002/0471250953.bi1212s49","DOIUrl":"10.1002/0471250953.bi1212s49","url":null,"abstract":"RNA editing is a post-transcriptional/co-transcriptional molecular phenomenon whereby a genetic message is modified from the corresponding DNA template by means of substitutions, insertions, and/or deletions. It occurs in a variety of organisms and different cellular locations through evolutionally and biochemically unrelated proteins. RNA editing has a plethora of biological effects including the modulation of alternative splicing and fine-tuning of gene expression. RNA editing events by base substitutions can be detected on a genomic scale by NGS technologies through the REDItools package, an ad hoc suite of Python scripts to study RNA editing using RNA-Seq and DNA-Seq data or RNA-Seq data alone. REDItools implement effective filters to minimize biases due to sequencing errors, mapping errors, and SNPs. The package is freely available at Google Code repository (http://code.google.com/p/reditools/) and released under the MIT license. In the present unit we show three basic protocols corresponding to three main REDItools scripts. © 2015 by John Wiley & Sons, Inc.","PeriodicalId":10958,"journal":{"name":"Current protocols in bioinformatics","volume":"49 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/0471250953.bi1212s49","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32992294","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 32

Scoring Large-Scale Affinity Purification Mass Spectrometry Datasets with MiST 用MiST评分大规模亲和纯化质谱数据集

Current protocols in bioinformatics Pub Date : 2018-02-15 DOI: 10.1002/0471250953.bi0819s49

Erik Verschueren, John Von Dollen, Peter Cimermancic, Natali Gulbahce, Andrej Sali, Nevan J. Krogan

引用次数: 57

Data Analysis Pipeline for RNA-seq Experiments: From Differential Expression to Cryptic Splicing RNA-seq实验的数据分析管道:从差异表达到隐剪接

Current protocols in bioinformatics Pub Date : 2018-02-13 DOI: 10.1002/cpbi.33

Hari Krishna Yalamanchili, Ying-Wooi Wan, Zhandong Liu

{"title":"Data Analysis Pipeline for RNA-seq Experiments: From Differential Expression to Cryptic Splicing","authors":"Hari Krishna Yalamanchili, Ying-Wooi Wan, Zhandong Liu","doi":"10.1002/cpbi.33","DOIUrl":"10.1002/cpbi.33","url":null,"abstract":"RNA sequencing (RNA-seq) is a high-throughput technology that provides unique insights into the transcriptome. It has a wide variety of applications in quantifying genes/isoforms and in detecting non-coding RNA, alternative splicing, and splice junctions. It is extremely important to comprehend the entire transcriptome for a thorough understanding of the cellular system. Several RNA-seq analysis pipelines have been proposed to date. However, no single analysis pipeline can capture dynamics of the entire transcriptome. Here, we compile and present a robust and commonly used analytical pipeline covering the entire spectrum of transcriptome analysis, including quality checks, alignment of reads, differential gene/transcript expression analysis, discovery of cryptic splicing events, and visualization. Challenges, critical parameters, and possible downstream functional analysis pipelines associated with each step are highlighted and discussed. This unit provides a comprehensive understanding of state-of-the-art RNA-seq analysis pipeline and a greater understanding of the transcriptome. © 2017 by John Wiley & Sons, Inc.","PeriodicalId":10958,"journal":{"name":"Current protocols in bioinformatics","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpbi.33","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35402458","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 35

Using the Contextual Hub Analysis Tool (CHAT) in Cytoscape to Identify Contextually Relevant Network Hubs 在Cytoscape中使用上下文枢纽分析工具(CHAT)来识别上下文相关的网络枢纽

Current protocols in bioinformatics Pub Date : 2018-02-13 DOI: 10.1002/cpbi.35

Tanja Muetze, David J. Lynn

引用次数: 5

Using SQL Databases for Sequence Similarity Searching and Analysis 基于SQL数据库的序列相似性搜索与分析

Current protocols in bioinformatics Pub Date : 2018-02-13 DOI: 10.1002/cpbi.32

William R. Pearson, Aaron J. Mackey

{"title":"Using SQL Databases for Sequence Similarity Searching and Analysis","authors":"William R. Pearson, Aaron J. Mackey","doi":"10.1002/cpbi.32","DOIUrl":"10.1002/cpbi.32","url":null,"abstract":"Relational databases can integrate diverse types of information and manage large sets of similarity search results, greatly simplifying genome-scale analyses. By focusing on taxonomic subsets of sequences, relational databases can reduce the size and redundancy of sequence libraries and improve the statistical significance of homologs. In addition, by loading similarity search results into a relational database, it becomes possible to explore and summarize the relationships between all of the proteins in an organism and those in other biological kingdoms. This unit describes how to use relational databases to improve the efficiency of sequence similarity searching and demonstrates various large-scale genomic analyses of homology-related data. It also describes the installation and use of a simple protein sequence database, seqdb_demo, which is used as a basis for the other protocols. The unit also introduces search_demo, a database that stores sequence similarity search results. The search_demo database is then used to explore the evolutionary relationships between E. coli proteins and proteins in other organisms in a large-scale comparative genomic analysis. © 2017 by John Wiley & Sons, Inc.","PeriodicalId":10958,"journal":{"name":"Current protocols in bioinformatics","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2018-02-13","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1002/cpbi.32","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35402459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 6

Finding Homologs in Amino Acid Sequences Using Network BLAST Searches 利用网络BLAST搜索在氨基酸序列中寻找同源物

Current protocols in bioinformatics Pub Date : 2018-02-13 DOI: 10.1002/cpbi.34

Istvan Ladunga

引用次数: 8

Using ProteomeScout: A Resource of Post-Translational Modifications, Their Experiments, and the Proteins That They Annotate 使用ProteomeScout:翻译后修饰的资源，他们的实验，和他们注释的蛋白质

Current protocols in bioinformatics Pub Date : 2018-02-13 DOI: 10.1002/cpbi.31

Arshag D. Mooradian, Jason M. Held, Kristen M. Naegle

引用次数: 5