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Method: Evaluation of strategies for evidence-driven genome annotation using long-read RNA-seq
- Alejandro Paniagua,
- Cristina Agustín-García,
- Francisco J. Pardo-Palacios,
- Thomas Brown,
- Maite De Maria,
- Nancy D. Denslow,
- Camila J. Mazzoni,
- and Ana Conesa
Genome Res. April 2025 35: 1053-1064; Published in Advance December 23, 2024, doi:10.1101/gr.279864.124
...). For benchmarking purposes, we used the well-annotated human and long-read cDNA reads of the human cell line WTC11 generated by the Long-read RNA-seq Genome Annotation Assessment Project (LRGASP) (Pardo-Palacios et al. 2024b). We exemplify the utility of the best-performing approach on the annotation...
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Method: BRAKER3: Fully automated genome annotation using RNA-seq and protein evidence with GeneMark-ETP, AUGUSTUS, and TSEBRA
- Lars Gabriel,
- Tomáš Brůna,
- Katharina J. Hoff,
- Matthis Ebel,
- Alexandre Lomsadze,
- Mark Borodovsky,
- and Mario Stanke
Genome Res. May 2024 34: 769-777; Published in Advance June 12, 2024, doi:10.1101/gr.278090.123
...://www.earthbio.org), which aims to annotate approximately 1.5 million eukaryotic species, further require that the annotation pipeline is highly automated and reliable, and ideally, no manual work for each species is required when assembly and RNA-seq are given.Further, species that have an annotation also require...
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Resource: Generation and analysis of a mouse multitissue genome annotation atlas
- Matthew Adams and
- Christopher Vollmers
Genome Res. November 2024 34: 2108-2117; Published in Advance October 23, 2024, doi:10.1101/gr.279217.124
...annotation should contain information on what tissues express what transcript isoforms at what level. This tissue-level isoform information can then inform a wide range of research questions as well as experiment designs. Long-read sequencing technology combined with advanced full-length cDNA library...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...sequence tags (ESTs) and cDNAs, with fewer than 0.5 M cDNAs and ∼8.5 M ESTs ever captured. In an era of relative data sparsity, annotating every transcript detected was a plausible goal notwithstanding the immaturity of much of the software and computational tooling supporting the annotation effort...
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Method: GeneMark-ETP significantly improves the accuracy of automatic annotation of large eukaryotic genomes
- Tomáš Brůna,
- Alexandre Lomsadze,
- and Mark Borodovsky
Genome Res. May 2024 34: 757-768; Published in Advance June 12, 2024, doi:10.1101/gr.278373.123
...in the assessment of the accuracy of gene prediction are more stringent; they require exact matches of predicted and annotated CDSs. Although BUSCO scores are overly optimistic if used for assessment of gene-prediction quality, they are certainly helpful for the coarse evaluation of completeness of assembly...
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Resource: Construction and evaluation of a new rat reference genome assembly, GRCr8, from long reads and long-range scaffolding
- Kai Li,
- Melissa L. Smith,
- J. Chris Blazier,
- Kelli J. Kochan,
- Jonathan M.D. Wood,
- Kerstin Howe,
- Anne E. Kwitek,
- Melinda R. Dwinell,
- Hao Chen,
- Julia L. Ciosek,
- Patrick Masterson,
- Terence D. Murphy,
- Theodore S. Kalbfleisch,
- and Peter A. Doris
Genome Res. November 2024 34: 2081-2093; Published in Advance November 8, 2024, doi:10.1101/gr.279292.124
...a comparison and includes equivalent data for the current mouse reference assembly GRCm39 (NCBI Mus musculus annotation release 109). Although the mouse assembly annotation arises from a different data set of mouse RefSeq sequences, which includes a larger accumulation of cDNA and other sequencing data...
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Method: Comparative Annotation Toolkit (CAT)—simultaneous clade and personal genome annotation
- Ian T. Fiddes,
- Joel Armstrong,
- Mark Diekhans,
- Stefanie Nachtweide,
- Zev N. Kronenberg,
- Jason G. Underwood,
- David Gordon,
- Dent Earl,
- Thomas Keane,
- Evan E. Eichler,
- David Haussler,
- Mario Stanke,
- and Benedict Paten
Genome Res. July 2018 28: 1029-1038; Published in Advance June 8, 2018, doi:10.1101/gr.233460.117
...alignments. Bioinformatics 29: 1341–1342. ↵Hoff K, Stanke M. 2015. Current methods for automated annotation of protein-coding genes. Curr Opin Insect Sci 7: 8–14. ↵Holt C, Yandell M. 2011. MAKER2: an annotation pipeline and -database management tool for second-generation projects. BMC Bioinformatics 12: 491...
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Method: Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes
- T.S. Keshava Prasad,
- Ajeet Kumar Mohanty,
- Manish Kumar,
- Sreelakshmi K. Sreenivasamurthy,
- Gourav Dey,
- Raja Sekhar Nirujogi,
- Sneha M. Pinto,
- Anil K. Madugundu,
- Arun H. Patil,
- Jayshree Advani,
- Srikanth S. Manda,
- Manoj Kumar Gupta,
- Sutopa B. Dwivedi,
- Dhanashree S. Kelkar,
- Brantley Hall,
- Xiaofang Jiang,
- Ashley Peery,
- Pavithra Rajagopalan,
- Soujanya D. Yelamanchi,
- Hitendra S. Solanki,
- Remya Raja,
- Gajanan J. Sathe,
- Sandip Chavan,
- Renu Verma,
- Krishna M. Patel,
- Ankit P. Jain,
- Nazia Syed,
- Keshava K. Datta,
- Aafaque Ahmed Khan,
- Manjunath Dammalli,
- Savita Jayaram,
- Aneesha Radhakrishnan,
- Christopher J. Mitchell,
- Chan-Hyun Na,
- Nirbhay Kumar,
- Photini Sinnis,
- Igor V. Sharakhov,
- Charles Wang,
- Harsha Gowda,
- Zhijian Tu,
- Ashwani Kumar,
- and Akhilesh Pandey
Genome Res. January 2017 27: 133-144; Published in Advance November 15, 2016, doi:10.1101/gr.201368.115
....1, respectively. cDNA sequences of 50 novel genes identified against the previous An. stephensi assembly annotations (ASTEI1) from VectorBase have been submitted to dbEST (https://www. ncbi.nlm.nih.gov/nucest) under the GenBank accession numbers JZ152704.1–JZ152780.1. Acknowledgments This paper is funded...
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LETTER: CDS Annotation in Full-Length cDNA Sequence
- Masaaki Furuno,
- Takeya Kasukawa,
- Rintaro Saito,
- Jun Adachi,
- Harukazu Suzuki,
- Richard Baldarelli,
- Yoshihide Hayashizaki,
- and Yasushi Okazaki
Genome Res. June 2003 13: 1478-1487; doi:10.1101/gr.1060303
...FANTOM2-MATRICS (Mouse Annotation Teleconference for RIKEN cDNA sequences; The FANTOM Consortium and the RIKEN Genome Exploration Research Group Phase I &amp; II Team 2002 ). The primary goals of MATRICS were to provide human-evaluated computational gene assignments (i.e., most informative gene names...
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Resource: GENCODE: The reference human genome annotation for The ENCODE Project
- Jennifer Harrow,
- Adam Frankish,
- Jose M. Gonzalez,
- Electra Tapanari,
- Mark Diekhans,
- Felix Kokocinski,
- Bronwen L. Aken,
- Daniel Barrell,
- Amonida Zadissa,
- Stephen Searle,
- If Barnes,
- Alexandra Bignell,
- Veronika Boychenko,
- Toby Hunt,
- Mike Kay,
- Gaurab Mukherjee,
- Jeena Rajan,
- Gloria Despacio-Reyes,
- Gary Saunders,
- Charles Steward,
- Rachel Harte,
- Michael Lin,
- Cédric Howald,
- Andrea Tanzer,
- Thomas Derrien,
- Jacqueline Chrast,
- Nathalie Walters,
- Suganthi Balasubramanian,
- Baikang Pei,
- Michael Tress,
- Jose Manuel Rodriguez,
- Iakes Ezkurdia,
- Jeltje van Baren,
- Michael Brent,
- David Haussler,
- Manolis Kellis,
- Alfonso Valencia,
- Alexandre Reymond,
- Mark Gerstein,
- Roderic Guigó,
- and Tim J. Hubbard
Genome Res. September 2012 22: 1760-1774; doi:10.1101/gr.135350.111
.... The finished genomic sequence is analyzed using a modified Ensembl pipeline (Searle et al. 2004), and BLAST results of cDNAs/ ESTs and proteins, along with various ab initio predictions, can be analyzedmanually in the annotation browser toolOtterlace (http:// www...
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