# Genome Annotation with MAKER
Diego Urquia

1. **Alignment to an already annotated genome**
2. Genome assembly - **ab initio** approach: signal predication (start and stop codons, splicing sites), content analysis (coding vs non coding), ab inition gene prediction (Augustus, GeneMark, fgenesh)

MAKER pipline components
Pearl, RepeatMasker, SNAP (ab initio), NCBI BLAST and exonerate (last two are reference-based)