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Gene Prediction

Methods and Protocols

  • Book
  • © 2019

Overview

Editors:
  1. Martin Kollmar

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

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  • 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
    Download chapter PDF

  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. Practical Guide for Fungal Gene Prediction from Genome Assembly and RNA-Seq Reads by FunGAP

    • Byoungnam Min, In-Geol Choi
    Pages 53-64

  6. Whole-Genome Annotation with BRAKER

    • Katharina J. Hoff, Alexandre Lomsadze, Mark Borodovsky, Mario Stanke
    Pages 65-95

  7. EuGene: An Automated Integrative Gene Finder for Eukaryotes and Prokaryotes

    • Erika Sallet, Jérôme Gouzy, Thomas Schiex
    Pages 97-120

  8. ChemGenome2.1: An Ab Initio Gene Prediction Software

    • Akhilesh Mishra, Priyanka Siwach, Poonam Singhal, B. Jayaram
    Pages 121-138

  9. Multi-Genome Annotation with AUGUSTUS

    • Stefanie Nachtweide, Mario Stanke
    Pages 139-160

  10. GeMoMa: Homology-Based Gene Prediction Utilizing Intron Position Conservation and RNA-seq Data

    • Jens Keilwagen, Frank Hartung, Jan Grau
    Pages 161-177

  11. Coding Exon-Structure Aware Realigner (CESAR): Utilizing Genome Alignments for Comparative Gene Annotation

    • Virag Sharma, Michael Hiller
    Pages 179-191

  12. Predicting Genes in Closely Related Species with Scipio and WebScipio

    • Martin Kollmar
    Pages 193-206

  13. 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

  14. Generating Publication-Ready Prokaryotic Genome Annotations with DFAST

    • Yasuhiro Tanizawa, Takatomo Fujisawa, Masanori Arita, Yasukazu Nakamura
    Pages 215-226

  15. BUSCO: Assessing Genome Assembly and Annotation Completeness

    • Mathieu Seppey, Mosè Manni, Evgeny M. Zdobnov
    Pages 227-245

  16. Evaluating Genome Assemblies and Gene Models Using gVolante

    • Osamu Nishimura, Yuichiro Hara, Shigehiro Kuraku
    Pages 247-256

  17. Choosing the Best Gene Predictions with GeneValidator

    • Ismail Moghul, Anurag Priyam, Yannick Wurm
    Pages 257-267

  18. COGNATE: Comparative Gene Annotation Characterizer

    • Jeanne Wilbrandt
    Pages 269-281

  19. Correction to: Choosing the Best Gene Predictions with GeneValidator

    • Ismail Moghul, Anurag Priyam, Yannick Wurm
    Pages C1-C1

  20. Back Matter

    Pages 283-284
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Keywords

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

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