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Select item 92854601.

QIIME 2 Enables Comprehensive End‐to‐End Analysis of Diverse Microbiome Data and Comparative Studies with Publicly Available Data

Mehrbod Estaki, Lingjing Jiang, Nicholas A. Bokulich, Daniel McDonald, Antonio González, Tomasz Kosciolek, Cameron Martino, Qiyun Zhu, Amanda Birmingham, Yoshiki Vázquez‐Baeza, Matthew R. Dillon, Evan Bolyen, J. Gregory Caporaso, Rob Knight

Curr Protoc Bioinformatics. 2020 Jun; 70(1): e100. Published online 2020 Apr 28. doi: 10.1002/cpbi.100

PMCID:: PMC9285460

Article PDF–3.1M

Select item 73788892.

NCBI's Conserved Domain Database and Tools for Protein Domain Analysis

Mingzhang Yang, Myra K. Derbyshire, Roxanne A. Yamashita, Aron Marchler‐Bauer

Curr Protoc Bioinformatics. 2020 Mar; 69(1): e90. Published online 2019 Dec 18. doi: 10.1002/cpbi.90

PMCID:: PMC7378889

Article PDF–7.6M

Select item 67546223.

Non-coding RNA analysis using the Rfam database

Ioanna Kalvari, Eric P. Nawrocki, Joanna Argasinska, Natalia Quinones-Olvera, Robert D. Finn, Alex Bateman, Anton I. Petrov

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2019 Sep 21.

Published in final edited form as: Curr Protoc Bioinformatics. 2018 Jun; 62(1): e51. Published online 2018 Jun 5. doi: 10.1002/cpbi.51

PMCID:: PMC6754622

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Select item 57264564.

Protein 3D Structure and Electron Microscopy Map Retrieval Using 3D-SURFER2.0 and EM-SURFER

Xusi Han, Qing Wei, Daisuke Kihara

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2018 Dec 8.

Published in final edited form as: Curr Protoc Bioinformatics. 2017 Dec 8; 60: 3.14.1–3.14.15. Published online 2017 Dec 8. doi: 10.1002/cpbi.37

PMCID:: PMC5726456

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Select item 63738695.

Data analysis pipeline for RNA-seq experiments: From differential expression to cryptic splicing

Hari Krishna Yalamanchili, Ying-Wooi Wan, Zhandong Liu

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2019 Feb 13.

Published in final edited form as: Curr Protoc Bioinformatics. 2017 Sep 13; 59: 11.15.1–11.15.21. Published online 2017 Sep 13. doi: 10.1002/cpbi.33

PMCID:: PMC6373869

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Select item 60976056.

cgpCaVEManWrapper: Simple Execution of CaVEMan in Order to Detect Somatic Single Nucleotide Variants in NGS Data

David Jones, Keiran M. Raine, Helen Davies, Patrick S. Tarpey, Adam P. Butler, Jon W. Teague, Serena Nik-Zainal, Peter J. Campbell

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2018 Aug 17.

Published in final edited form as: Curr Protoc Bioinformatics. 2016 Dec 8; 56: 15.10.1–15.10.18. Published online 2016 Dec 8. doi: 10.1002/cpbi.20

PMCID:: PMC6097605

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Select item 51526917.

Exploring FlyBase Data Using QuickSearch

Steven J. Marygold, Giulia Antonazzo, Helen Attrill, Marta Costa, Madeline A. Crosby, Gilberto dos Santos, Joshua L. Goodman, L. Sian Gramates, Beverley B. Matthews, Alix J. Rey, Jim Thurmond, The FlyBase Consortium

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2017 Dec 8.

Published in final edited form as: Curr Protoc Bioinformatics. 2016 Dec 8; 56: 1.31.1–1.31.23. Published online 2016 Dec 8. doi: 10.1002/cpbi.19

PMCID:: PMC5152691

Article PDF–2.7M

Select item 51477508.

Searching the Mouse Genome Informatics (MGI) resources for information on mouse biology from genotype to phenotype

David Shaw

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2017 Dec 8.

Published in final edited form as: Curr Protoc Bioinformatics. 2016 Dec 8; 56: 1.7.1–1.7.16. Published online 2016 Dec 8. doi: 10.1002/cpbi.18

PMCID:: PMC5147750

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Select item 50101419.

Studying RNA homology and conservation with Infernal: from single sequences to RNA families

Lars Barquist, Sarah W. Burge, Paul P. Gardner

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2016 Dec 20.

Published in final edited form as: Curr Protoc Bioinformatics. 2016; 54: 12.13.1–12.13.25. Published online 2016 Jun 20. doi: 10.1002/cpbi.4

PMCID:: PMC5010141

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Select item 610119210.

VAGrENT: Variation Annotation Generator

Andy Menzies, Jon W. Teague, Adam P. Butler, Helen Davies, Patrick Tarpey, Serena Nik-Zainal, Peter J. Campbell

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2018 Aug 20.

Published in final edited form as: Curr Protoc Bioinformatics. 2015 Dec 17; 52: 15.8.1–15.811. Published online 2015 Dec 17. doi: 10.1002/0471250953.bi1508s52

PMCID:: PMC6101192

Article PDF–274K

Select item 609760611.

cgpPindel: Identifying Somatically Acquired Insertion and Deletion Events from Paired End Sequencing

Keiran M. Raine, Jonathan Hinton, Adam P. Butler, Jon W. Teague, Helen Davies, Patrick Tarpey, Serena Nik-Zainal, Peter J. Campbell

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2018 Aug 17.

Published in final edited form as: Curr Protoc Bioinformatics. 2015 Dec 17; 52: 15.7.1–15.712. Published online 2015 Dec 17. doi: 10.1002/0471250953.bi1507s52

PMCID:: PMC6097606

Article PDF–864K

Select item 487181812.

Protein Structure and Function Prediction Using I-TASSER

Jianyi Yang, Yang Zhang

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2016 May 19.

Published in final edited form as: Curr Protoc Bioinformatics. 2015; 52: 5.8.1–5.815. Published online 2015 Dec 17. doi: 10.1002/0471250953.bi0508s52

PMCID:: PMC4871818

Article PDF–964K

Select item 452246513.

Searching and navigating UniProt databases

Sangya Pundir, Michele Magrane, Maria J. Martin, Claire O’Donovan, The UniProt Consortium

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2016 Jun 19.

Published in final edited form as: Curr Protoc Bioinformatics. 2015; 50: 1.27.1–1.27.10. Published online 2015 Jun 19. doi: 10.1002/0471250953.bi0127s50

PMCID:: PMC4522465

Article PDF–1.4M

Select item 440700714.

Expression Data Analysis with Reactome

Steve Jupe, Antonio Fabregat, Henning Hermjakob

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2016 Mar 9.

Published in final edited form as: Curr Protoc Bioinformatics. 2015; 49: 8.20.1–8.20.9. Published online 2015 Mar 9. doi: 10.1002/0471250953.bi0820s49

PMCID:: PMC4407007

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Select item 431201515.

Using EMBL-EBI services via Web interface and programmatically via Web Services

Rodrigo Lopez, Andrew Cowley, Weizhong Li, Hamish McWilliam

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2015 Dec 12.

Published in final edited form as: Curr Protoc Bioinformatics. 2014; 48: 3.12.1–3.12.50. Published online 2014 Dec 12. doi: 10.1002/0471250953.bi0312s48

PMCID:: PMC4312015

Article PDF–7.1M

Select item 428637416.

Genome Annotation and Curation Using MAKER and MAKER-P

Michael S. Campbell, Carson Holt, Barry Moore, Mark Yandell

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2015 Dec 12.

Published in final edited form as: Curr Protoc Bioinformatics. 2014; 48: 4.11.1–4.11.39. Published online 2014 Dec 12. doi: 10.1002/0471250953.bi0411s48

PMCID:: PMC4286374

Article PDF–1.1M

Select item 421395617.

BEDTools: the Swiss-army tool for genome feature analysis

Aaron R. Quinlan

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2015 Sep 8.

Published in final edited form as: Curr Protoc Bioinformatics. 2014; 47: 11.12.1–11.12.34. Published online 2014 Sep 8. doi: 10.1002/0471250953.bi1112s47

PMCID:: PMC4213956

Article PDF–1.5M

Select item 433107318.

Using PeptideAtlas, SRMAtlas and PASSEL – Comprehensive Resources for discovery and targeted proteomics

Ulrike Kusebauch, Eric W. Deutsch, David S. Campbell, Zhi Sun, Terry Farrah, Robert L. Moritz

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2015 Jun 17.

Published in final edited form as: Curr Protoc Bioinformatics. 2014; 46: 13.25.1–13.25.28. Published online 2014 Jun 17. doi: 10.1002/0471250953.bi1325s46

PMCID:: PMC4331073

Article PDF–4.2M

Select item 411372819.

Employing ProteoWizard to Convert Raw Mass Spectrometry Data

Jerry D. Holman, David L. Tabb, Parag Mallick

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2015 Jun 17.

Published in final edited form as: Curr Protoc Bioinformatics. 2014; 46: 13.24.1–13.24.9. Published online 2014 Jun 17. doi: 10.1002/0471250953.bi1324s46

PMCID:: PMC4113728

Article PDF–384K

Select item 424252120.

Using SomaticSniper to Detect Somatic Single Nucleotide Variants

David E. Larson, Travis E. Abbott, Richard K. Wilson

Curr Protoc Bioinformatics. Author manuscript; available in PMC 2015 Mar 21.

Published in final edited form as: Curr Protoc Bioinformatics. 2014 Mar 21; 15(155): 15.5.1–15.5.8. Published online 2014 Mar 21. doi: 10.1002/0471250953.bi1505s45

PMCID:: PMC4242521

Article PDF–241K

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