Gene prediction: methods and protocols
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...
Gespeichert in:
| Weitere Verfasser: | |
|---|---|
| Format: | Elektronisch E-Book |
| Sprache: | English |
| Veröffentlicht: |
New York, NY
Springer New York
2019
|
| Ausgabe: | 1st ed. 2019 |
| Schriftenreihe: | Methods in Molecular Biology
1962 |
| Schlagworte: | |
| Online-Zugang: | UBR01 TUM01 Volltext |
| Zusammenfassung: | 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 |
| Beschreibung: | 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 |
| Beschreibung: | 1 Online-Ressource (XI, 284 Seiten) Illustrationen |
| ISBN: | 9781493991730 |
| DOI: | 10.1007/978-1-4939-9173-0 |
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| dewey-full | 570.285 |
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| discipline | Biologie |
| discipline_str_mv | Biologie |
| doi_str_mv | 10.1007/978-1-4939-9173-0 |
| edition | 1st ed. 2019 |
| format | Electronic eBook |
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| id | DE-604.BV047646742 |
| illustrated | Not Illustrated |
| index_date | 2024-07-03T18:48:56Z |
| indexdate | 2024-07-10T09:18:12Z |
| institution | BVB |
| isbn | 9781493991730 |
| language | English |
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| publisher | Springer New York |
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| series2 | Methods in Molecular Biology 1962 |
| spelling | Gene prediction methods and protocols edited by Martin Kollmar 1st ed. 2019 New York, NY Springer New York 2019 1 Online-Ressource (XI, 284 Seiten) Illustrationen txt rdacontent c rdamedia cr rdacarrier Methods in Molecular Biology 1962 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 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 Bioinformatics Medical genetics Kollmar, Martin ca. 20./21. Jh. (DE-588)115341743X edt Erscheint auch als Druck-Ausgabe 978-1-4939-9174-7 https://doi.org/10.1007/978-1-4939-9173-0 Verlag URL des Erstveröffentlichers Volltext |
| spellingShingle | Gene prediction methods and protocols Bioinformatics Medical genetics |
| title | Gene prediction methods and protocols |
| title_auth | Gene prediction methods and protocols |
| title_exact_search | Gene prediction methods and protocols |
| title_exact_search_txtP | Gene prediction methods and protocols |
| title_full | Gene prediction methods and protocols edited by Martin Kollmar |
| title_fullStr | Gene prediction methods and protocols edited by Martin Kollmar |
| title_full_unstemmed | Gene prediction methods and protocols edited by Martin Kollmar |
| title_short | Gene prediction |
| title_sort | gene prediction methods and protocols |
| title_sub | methods and protocols |
| topic | Bioinformatics Medical genetics |
| topic_facet | Bioinformatics Medical genetics |
| url | https://doi.org/10.1007/978-1-4939-9173-0 |
| work_keys_str_mv | AT kollmarmartin genepredictionmethodsandprotocols |