Gene Prediction : Methods and Protocols / edited by Martin Kollmar.

Format:

Book

Contributor:

Kollmar, Martin, editor.

SpringerLink (Online service)

Series:

Springer Protocols (Springer-12345)

Methods in molecular biology 1064-3745 ; 1962.

Methods in Molecular Biology, 1064-3745 ; 1962

Language:

English

Subjects (All):

Bioinformatics.

Medical genetics.

Gene Function.

Local Subjects:

Bioinformatics.

Gene Function.

Physical Description:

1 online resource (XI, 284 pages) : 54 illustrations, 49 illustrations in color.

Edition:

First edition 2019.

Contained In:

Springer eBooks

Place of Publication:

New York, NY : Springer New York : Imprint: Humana, 2019.

System Details:

text file PDF

Summary:

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:

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.

Other Format:

Printed edition:

ISBN:

978-1-4939-9173-0

9781493991730

Access Restriction:

Restricted for use by site license.