<p><span style="font-size:14px">Historically, sequencing was done in&nbsp;sequencing centers, centralized facilities (ranging from large independent institutions such as Joint Genome Institute&nbsp;which sequence dozens of terabases a year, to local molecular biology core facilities) which contain research laboratories with the costly instrumentation and technical support necessary. As sequencing technology continues to improve, however, a new generation of effective fast turnaround benchtop sequencers has come within reach of the average academic laboratory.<span style="line-height:17.3333px">&nbsp;</span>On the whole, genome sequencing approaches fall into two broad categories,&nbsp;shotgun&nbsp;and&nbsp;high-throughput&nbsp;(aka&nbsp;next-generation) sequencing.</span></p>

<p><span style="font-size:14px">The DNA sequence assembly alone is of little value without additional analysis.<span style="line-height:17.3333px">&nbsp;</span>Genome annotation&nbsp;is the process of attaching biological information to sequences,&nbsp;and consists of three main steps.&nbsp;① Identifying portions of the genome that do not code for proteins, ② Identifying elements on the genome,&nbsp;a process called gene prediction,&nbsp;and&nbsp;③ Attaching biological information to these elements.&nbsp;</span></p>

<p><span style="font-size:14px">Automatic annotation tools try to perform these steps in silico,&nbsp;as opposed to manual annotation which involves human expertise and potential experimental verification.&nbsp;Ideally, these approaches co-exist and complement each other in the same annotation pipeline.&nbsp;Traditionally, the basic level of annotation is using BLAST&nbsp;for finding similarities, and then annotating genomes based on homologues.<span style="line-height:17.3333px">&nbsp;</span>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&nbsp;rely on both curated data sources as well as a range of software tools in their automated genome annotation pipeline.&nbsp;Structural annotation&nbsp;consists of the identification of genomic elements, primarily ORFs&nbsp;and their localisation, or gene structure.&nbsp;Functional&nbsp;annotation&nbsp;consists of attaching biological information to genomic elements.</span></p>