Manual annotation is primarily from the Havana group at the Wellcome Trust Institute.
- Finished genomic sequence is analysed on a clone by clone basis using a combination of similarity searches against nucleotide and protein databases and ab initio gene predictions (GENSCAN, AUGUSTUS).
- In addition, sequence conservation data and a variety of DAS (Distributed Annotation System) tracks are loaded.
- The data thus gathered is then used to manually annotate genomic clones with gene and transcript structures and nomenclature and associated poly-A features.
- The annotation is based on supporting homology evidence only and includes all types of genes: protein coding, non-coding and pseudogenes.
- There is a fine-grained classification system for gene and transcript types (e.g. different types of pseudogenes, different types of non-coding RNAs).
Gene structures can also be generated by manual annotation from the community, for example the IRAG initiaitive in Pig. Annotation from these sources is perfomed under the guidance of the Havana group.