Gene Prediction, 1st ed. 2019
Methods and Protocols
Methods in Molecular Biology Series, Vol. 1962

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.

Preface…

Table of Contents…

Contributing Authors…

1. tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences

Patricia P. Chan and Todd M. Lowe

2. Predicting RNA Families In Nucleotides Sequences Using StructRNAfinder

Vinicius Maracaja-Coutinho, Raúl Arias-Carrasco, Helder I. Nakaya, and Victor Aliaga-Tobar

3. Structural and Functional Annotation of Eukaryotic Genomes with GenSAS

Jodi L. Humann, Taelin Lee, Stephen Ficklin, and Dorrie Main

Byoungnam Min and In-Geol Choi

5. Whole-Genome Annotation with BRAKER 

Katharina Hoff, Alexandre Lomsadze, Mark Borodovsky, and Mario Stanke

Erika Sallet, Jérôme Gouzy, and Thomas Schiex

7. ChemGenome2.1: An ab initio Gene Prediction Software

Akhilesh Mishra, Priyanka Siwach, Poonam Singhal, and B. Jayaram

Stefanie Nachtweide and Mario Stanke

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

Jens Keilwagen, Frank Hartung, and Jan Grau

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

Virag Sharma and Michael Hiller

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

Martin Kollmar

12. 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 Jiménez, and Antonio J. Pérez Pulido

13. Generating Publication-Ready Prokaryotic Genome Annotations with DFAST

Yasuhiro Tanizawa, Takatomo Fujisawa, Masanori Arita, and Yasukazu Nakamura

14. BUSCO: Assessing Genome Assembly and Annotation Completeness

Mathieu Seppey, Mosé Manni, and Evgeny M. Zbodnov

15. Evaluating Genome Assemblies and Gene Models using gVolante

Osamu Nishimura, Yuichiro Hara, and Shigehiro Kuraku

Ismail Moghul, Anurag Priyam, and Yannick Wurm

17. COGNATE: Comparative Gene Annotation Characterizer

Jeanne Wilbrandt