Editing Genomics (section)

=== Annotation ===
{{Main|Genome annotation}}
The DNA sequence assembly alone is of little value without additional analysis.<ref name = "Pevsner_2009"/> Genome annotation is the process of attaching biological information to [[DNA sequence|sequences]], and consists of three main steps:<ref name = "Stein_2001"/>
# identifying portions of the genome that do not code for proteins
# identifying elements on the [[genome]], a process called [[gene prediction]], and
# attaching biological information to these elements.
Automatic annotation tools try to perform these steps ''[[in silico]]'', as opposed to manual annotation (a.k.a. curation) which involves human expertise and potential experimental verification.<ref name = "Brent_2008"/> Ideally, these approaches co-exist and complement each other in the same annotation [[Pipeline (computing)|pipeline]] (also see [[#Sequencing pipelines|below]]).

Traditionally, the basic level of annotation is using [[BLAST (biotechnology)|BLAST]] for finding similarities, and then annotating genomes based on homologues.<ref name = "Pevsner_2009"/> More recently, additional information is added to the annotation platform. The additional information allows manual annotators to deconvolute discrepancies between genes that are given the same annotation. Some databases use genome context information, similarity scores, experimental data, and integrations of other resources to provide genome annotations through their Subsystems approach. Other databases (e.g. [[Ensembl]]) rely on both curated data sources as well as a range of software tools in their automated genome annotation pipeline.<ref name = "Ensmbl_2013"/> ''Structural annotation'' consists of the identification of genomic elements, primarily [[Open reading frame|ORFs]] and their localisation, or gene structure. ''Functional annotation'' consists of attaching biological information to genomic elements.