Minoche, Andre E; Dohm, Juliane C; Schneider, Jessica; Holtgräwe, Daniela; Viehöver, Prisca; Montfort, Magda; Rosleff Sörensen, Thomas; Weisshaar, Bernd; Himmelbauer, Heinz: Exploiting single-molecule transcript sequencing for eukaryotic gene prediction. In: Genome Biology. Jg.16 H. 1. 2015
Inhalt
- Results and discussion
- Conclusions
- Methods
- Genome assemblies
- Sample preparation and SMRT sequencing
- Data analysis overview
- Pre-processing of SMRT reads
- Identification of SMRT reads containing full-length ORFs
- Correction of SMRT sequences
- Stress conditions and mRNA-seq data
- Identification of accurate sugar beet gene models for parameter training
- Training and testing gene prediction parameters
- Masking transposable elements
- Processing of expression evidence
- Calculation of an optimized sugar beet gene set
- Transferring stable sugar beet gene identifiers
- Manual quality assessment of gene predictions
- Calculating number of stress-condition specific genes
- Applying Beta vulgaris parameters on spinach gene prediction
- Prediction of 1:1 orthologous genes between sugar beet and spinach
- Data access
- Additional files
- Abbreviations
- Competing interests
- Authors’ contributions
- Acknowledgments
- Author details
- References