Assessment and refinement of eukaryotic gene structure prediction with gene-structure-aware multiple protein sequence alignment
Open Access
- 14 June 2014
- journal article
- Published by Springer Nature in BMC Bioinformatics
- Vol. 15 (1) , 189
- https://doi.org/10.1186/1471-2105-15-189
Abstract
Accurate computational identification of eukaryotic gene organization is a long-standing problem. Despite the fundamental importance of precise annotation of genes encoded in newly sequenced genomes, the accuracy of predicted gene structures has not been critically evaluated, mostly due to the scarcity of proper assessment methods.Keywords
This publication has 49 references indexed in Scilit:
- Assessing the utility of coevolution-based residue–residue contact predictions in a sequence- and structure-rich eraProceedings of the National Academy of Sciences, 2013
- MisPred: a resource for identification of erroneous protein sequences in public databasesDatabase: The Journal of Biological Databases and Curation, 2013
- An integrated encyclopedia of DNA elements in the human genomeNature, 2012
- Direct-coupling analysis of residue coevolution captures native contacts across many protein familiesProceedings of the National Academy of Sciences, 2011
- Meeting report: a workshop on Best Practices in Genome AnnotationDatabase: The Journal of Biological Databases and Curation, 2010
- Genome 10K: A Proposal to Obtain Whole-Genome Sequence for 10 000 Vertebrate SpeciesJournal of Heredity, 2009
- Genomewide comparative analysis of alternative splicing in plantsProceedings of the National Academy of Sciences, 2006
- Comparative Protein Modelling by Satisfaction of Spatial RestraintsJournal of Molecular Biology, 1993
- The P450 Superfamily: Update on New Sequences, Gene Mapping, Accession Numbers, Early Trivial Names of Enzymes, and NomenclatureDNA and Cell Biology, 1993
- The rapid generation of mutation data matrices from protein sequencesBioinformatics, 1992