Name
Title | ||
|---|---|---|
Short-read reading-frame predictors are not created equal: sequence error causes loss of signal. |
Abstract | ||
|---|---|---|
Gene prediction algorithms (or gene callers) are an essential tool for analyzing shotgun nucleic acid sequence data. Gene prediction is a ubiquitous step in sequence analysis pipelines; it reduces the volume of data by identifying the most likely reading frame for a fragment, permitting the out-of-frame translations to be ignored. In this study we evaluate five widely used ab initio gene-calling algorithms—FragGeneScan, MetaGeneAnnotator, MetaGeneMark, Orphelia, and Prodigal—for accuracy on short (75–1000 bp) fragments containing sequence error from previously published artificial data and “real” metagenomic datasets. |
Year | DOI | Venue |
|---|---|---|
2012 | 10.1186/1471-2105-13-183 | BMC Bioinformatics |
Keywords | Field | DocType |
Gene prediction, Sequence errors, Short reads, Reading frames, Gene callers, Ab-initio gene prediction | Alignment-free sequence analysis,Biology,Gene prediction,Coding region,Metagenomics,Bioinformatics,Genetics,Molecular Sequence Annotation,DNA microarray,Sequence assembly,Sequence analysis | Journal |
Volume | Issue | ISSN |
13 | 1 | 1471-2105 |
Citations | PageRank | References |
11 | 0.58 | 19 |
Authors | ||
7 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| William L. Trimble | 1 | 33 | 2.87 |
| Kevin P. Keegan | 2 | 62 | 3.93 |
| Mark D'Souza | 3 | 18 | 1.30 |
| Andreas Wilke | 4 | 314 | 23.84 |
| Jared Wilkening | 5 | 48 | 3.77 |
| Jack A. Gilbert | 6 | 31 | 2.75 |
| Folker Meyer | 7 | 484 | 51.83 |