Describe the process of genome annotation.

Genome annotation identifies functional elements in a genome sequence. It involves: 1) Repeat masking - identify and mask repetitive elements using RepeatMasker. 2) Gene prediction - ab initio predictors (Augustus, GeneMark) use HMMs trained on known genes; evidence-based methods incorporate EST/RNA-Seq alignments and protein homology. MAKER and Braker combine approaches. 3) Functional annotation - assign gene names and functions through homology searches (BLAST), domain prediction (InterProScan), and pathway mapping (KEGG, GO). 4) Non-coding element annotation - identify rRNAs, tRNAs (tRNAscan), small RNAs, and regulatory elements. 5) Quality control and manual curation - validate predictions, resolve conflicts. Output formats include GFF3 and GenBank.