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Gene Prediction

Methods and Protocols

Editors:

  • Includes cutting-edge methods and protocols
  • Provides step-by-step detail essential for reproducible results
  • Contains key notes and implementation advice from the experts

Part of the book series: Methods in Molecular Biology (MIMB, volume 1962)

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Table of contents (18 protocols)

  1. Front Matter

    Pages i-xi
  2. tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences

    • Patricia P. Chan, Todd M. Lowe
    Pages 1-14
  3. Predicting RNA Families in Nucleotide Sequences Using StructRNAfinder

    • Vinicius Maracaja-Coutinho, Raúl Arias-Carrasco, Helder I. Nakaya, Victor Aliaga-Tobar
    Pages 15-27
  4. Structural and Functional Annotation of Eukaryotic Genomes with GenSAS

    • Jodi L. Humann, Taein Lee, Stephen Ficklin, Dorrie Main
    Pages 29-51Open Access
  5. Whole-Genome Annotation with BRAKER

    • Katharina J. Hoff, Alexandre Lomsadze, Mark Borodovsky, Mario Stanke
    Pages 65-95
  6. EuGene: An Automated Integrative Gene Finder for Eukaryotes and Prokaryotes

    • Erika Sallet, Jérôme Gouzy, Thomas Schiex
    Pages 97-120
  7. ChemGenome2.1: An Ab Initio Gene Prediction Software

    • Akhilesh Mishra, Priyanka Siwach, Poonam Singhal, B. Jayaram
    Pages 121-138
  8. Multi-Genome Annotation with AUGUSTUS

    • Stefanie Nachtweide, Mario Stanke
    Pages 139-160
  9. AnABlast: Re-searching for Protein-Coding Sequences in Genomic Regions

    • Alejandro Rubio, Carlos S. Casimiro-Soriguer, Pablo Mier, Miguel A. Andrade-Navarro, Andrés Garzón, Juan Jimenez et al.
    Pages 207-214
  10. Generating Publication-Ready Prokaryotic Genome Annotations with DFAST

    • Yasuhiro Tanizawa, Takatomo Fujisawa, Masanori Arita, Yasukazu Nakamura
    Pages 215-226
  11. BUSCO: Assessing Genome Assembly and Annotation Completeness

    • Mathieu Seppey, Mosè Manni, Evgeny M. Zdobnov
    Pages 227-245
  12. Evaluating Genome Assemblies and Gene Models Using gVolante

    • Osamu Nishimura, Yuichiro Hara, Shigehiro Kuraku
    Pages 247-256
  13. Choosing the Best Gene Predictions with GeneValidator

    • Ismail Moghul, Anurag Priyam, Yannick Wurm
    Pages 257-267
  14. Correction to: Choosing the Best Gene Predictions with GeneValidator

    • Ismail Moghul, Anurag Priyam, Yannick Wurm
    Pages C1-C1
  15. Back Matter

    Pages 283-284

About this book

This volume introduces software used for gene prediction with focus on eukaryotic genomes. The chapters in this book describe software and web server usage as applied in common use-cases, and explain ways to simplify re-annotation of long available genome assemblies. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary computational requirements, step-by-step, readily reproducible computational protocols, and tips on troubleshooting and avoiding known pitfalls.



Cutting-edge and thorough, Gene Prediction: Methods and Protocols is a valuable resource for researchers and research groups working on the assembly and annotation of single species or small groups of species. 


Chapter 3 is available open access under a CC BY 4.0 license via link.springer.com.


Editors and Affiliations

  • Group Systems Biology of Motor Proteins, Department NMR-based Structural Biology, Max-Planck-Institute for Biophysical Chemistry, Goettingen, Germany

    Martin Kollmar

Bibliographic Information

  • Book Title: Gene Prediction

  • Book Subtitle: Methods and Protocols

  • Editors: Martin Kollmar

  • Series Title: Methods in Molecular Biology

  • DOI: https://doi.org/10.1007/978-1-4939-9173-0

  • Publisher: Humana New York, NY

  • eBook Packages: Springer Protocols

  • Copyright Information: Springer Science+Business Media, LLC, part of Springer Nature 2019

  • Hardcover ISBN: 978-1-4939-9172-3Published: 25 April 2019

  • eBook ISBN: 978-1-4939-9173-0Published: 24 April 2019

  • Series ISSN: 1064-3745

  • Series E-ISSN: 1940-6029

  • Edition Number: 1

  • Number of Pages: XI, 284

  • Number of Illustrations: 5 b/w illustrations, 49 illustrations in colour

  • Topics: Bioinformatics, Gene Function

Buy it now

Buying options

eBook USD 149.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Hardcover Book USD 199.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Other ways to access