Main description:

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.

Contents:

Preface...Table of Contents...Contributing Authors...
1. tRNAscan-SE: Searching for tRNA Genes in Genomic SequencesPatricia P. Chan and Todd M. Lowe
2. Predicting RNA Families In Nucleotides Sequences Using StructRNAfinderVinicius Maracaja-Coutinho, Raul Arias-Carrasco, Helder I. Nakaya, and Victor Aliaga-Tobar
3. Structural and Functional Annotation of Eukaryotic Genomes with GenSASJodi L. Humann, Taelin Lee, Stephen Ficklin, and Dorrie Main
4. Practical Guide for Fungal Gene Prediction from Genome Assembly and RNA-seq Reads by FunGAPByoungnam Min and In-Geol Choi
5. Whole-Genome Annotation with BRAKER Katharina Hoff, Alexandre Lomsadze, Mark Borodovsky, and Mario Stanke
6. EuGene: An Automated Integrative Gene Finder for Eukaryotes and ProkaryotesErika Sallet, Jerome Gouzy, and Thomas Schiex
7. ChemGenome2.1: An ab initio Gene Prediction SoftwareAkhilesh Mishra, Priyanka Siwach, Poonam Singhal, and B. Jayaram
8. Multi-Genome Annotation with AUGUSTUSStefanie Nachtweide and Mario Stanke
9. GeMoMa: Homology-Based Gene Prediction Utilizing Intron Position Conservation and RNA-seq DataJens Keilwagen, Frank Hartung, and Jan Grau
10. Coding Exon-Structure Aware Realigner (CESAR): Utilizing Genome Alignments for Comparative Gene AnnotationVirag Sharma and Michael Hiller
11. Predicting Genes in Closely Related Species with Scipio and WebScipioMartin Kollmar
12. AnABlast, Re-Searching for Protein-Coding Sequences in Genomic RegionsAlejandro Rubio, Carlos S. Casimiro-Soriguer, Pablo Mier, Miguel A. Andrade-Navarro, Andres Garzon, Juan Jimenez, and Antonio J. Perez Pulido
13. Generating Publication-Ready Prokaryotic Genome Annotations with DFASTYasuhiro Tanizawa, Takatomo Fujisawa, Masanori Arita, and Yasukazu Nakamura
14. BUSCO: Assessing Genome Assembly and Annotation CompletenessMathieu Seppey, Mose Manni, and Evgeny M. Zbodnov
15. Evaluating Genome Assemblies and Gene Models using gVolanteOsamu Nishimura, Yuichiro Hara, and Shigehiro Kuraku
16. Choosing the Best Gene Predictions with GeneValidatorIsmail Moghul, Anurag Priyam, and Yannick Wurm
17. COGNATE: Comparative Gene Annotation CharacterizerJeanne Wilbrandt