© 2019

Gene Prediction

Methods and Protocols

  • Martin Kollmar
  • 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 Methods in Molecular Biology book series (MIMB, volume 1962)

Table of contents

  1. Front Matter
    Pages i-xi
  2. Patricia P. Chan, Todd M. Lowe
    Pages 1-14
  3. Vinicius Maracaja-Coutinho, Raúl Arias-Carrasco, Helder I. Nakaya, Victor Aliaga-Tobar
    Pages 15-27
  4. Jodi L. Humann, Taein Lee, Stephen Ficklin, Dorrie Main
    Pages 29-51 Open Access
  5. Katharina J. Hoff, Alexandre Lomsadze, Mark Borodovsky, Mario Stanke
    Pages 65-95
  6. Erika Sallet, Jérôme Gouzy, Thomas Schiex
    Pages 97-120
  7. Akhilesh Mishra, Priyanka Siwach, Poonam Singhal, B. Jayaram
    Pages 121-138
  8. Stefanie Nachtweide, Mario Stanke
    Pages 139-160
  9. Alejandro Rubio, Carlos S. Casimiro-Soriguer, Pablo Mier, Miguel A. Andrade-Navarro, Andrés Garzón, Juan Jimenez et al.
    Pages 207-214
  10. Yasuhiro Tanizawa, Takatomo Fujisawa, Masanori Arita, Yasukazu Nakamura
    Pages 215-226
  11. Mathieu Seppey, Mosè Manni, Evgeny M. Zdobnov
    Pages 227-245
  12. Osamu Nishimura, Yuichiro Hara, Shigehiro Kuraku
    Pages 247-256
  13. Ismail Moghul, Anurag Priyam, Yannick Wurm
    Pages 257-267
  14. 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


mGene Computational Gene Finding Generalized Hidden Markov Model Protein-coding gene prediction C. elegans genes

Editors and affiliations

  • Martin Kollmar
    • 1
  1. 1.Group Systems Biology of Motor Proteins, Department NMR-based Structural BiologyMax-Planck-Institute for Biophysical ChemistryGoettingenGermany

Bibliographic information

  • Book Title Gene Prediction
  • Book Subtitle Methods and Protocols
  • Editors Martin Kollmar
  • Series Title Methods in Molecular Biology
  • Series Abbreviated Title Methods Molecular Biology
  • DOI
  • Copyright Information Springer Science+Business Media, LLC, part of Springer Nature 2019
  • Publisher Name Humana, New York, NY
  • eBook Packages Springer Protocols
  • Hardcover ISBN 978-1-4939-9172-3
  • eBook ISBN 978-1-4939-9173-0
  • 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 this book on publisher's site
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