What does MAKER do?
Identifies and masks out repeat elements
Aligns ESTs to the genome
Aligns proteins to the genome
Produces ab initio gene predictions
Synthesizes these data into final annotations
Produces evidence-based quality values for downstream annotation management
Examples of evidence supporting a structural annotation:
Ab initio gene predictions
Transcribed RNA (mRNA-Seq/ESTs/cDNA/transcript)
Proteins
By using ab inito gene predictors within the MAKER pipeline you get several key benefits:
MAKER provides gene models together with an evidence trail - useful for manual curation and quality control.
MAKER provides a framework within which you can train and retrain gene predictors for improved performance.
MAKER's output (including supporting evidence) can easily be loaded into a GMOD compatible database for annotation distribution.
MAKER's annotations can be easily updated with new evidence by passing existing annotation sets back though MAKER.