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.
Reihe
Auflage
Sprache
Verlagsort
Zielgruppe
Illustrationen
49
5 s/w Abbildungen, 49 farbige Abbildungen
XI, 284 p. 54 illus., 49 illus. in color.
Maße
Höhe: 260 mm
Breite: 183 mm
Dicke: 22 mm
Gewicht
ISBN-13
978-1-4939-9172-3 (9781493991723)
DOI
10.1007/978-1-4939-9173-0
Schweitzer Klassifikation
tRNAscan-SE: Searching for tRNA Genes in Genomic Sequences.- Predicting RNA Families In Nucleotides Sequences Using StructRNAfinder.- Structural and Functional Annotation of Eukaryotic Genomes with GenSAS.- Practical Guide for Fungal Gene Prediction from Genome Assembly and RNA-seq Reads by FunGAP.- Whole-Genome Annotation with BRAKER.- EuGene: An Automated Integrative Gene Finder for Eukaryotes and Prokaryotes.- ChemGenome2.1: An ab initio Gene Prediction Software.- Multi-Genome Annotation with AUGUSTUS.- GeMoMa: Homology-Based Gene Prediction Utilizing Intron Position Conservation and RNA-seq Data.- Coding Exon-Structure Aware Realigner (CESAR): Utilizing Genome Alignments for Comparative Gene Annotation.- Predicting Genes in Closely Related Species with Scipio and WebScipio.- AnABlast, Re-Searching for Protein-Coding Sequences in Genomic Regions.- Generating Publication-Ready Prokaryotic Genome Annotations with DFAST.- BUSCO: Assessing Genome Assembly and Annotation Completeness.- Evaluating Genome Assemblies and Gene Models using gVolante.- Choosing the Best Gene Predictions with GeneValidator.- COGNATE: Comparative Gene Annotation Characterizer.
