The first component of our annotation interface is the gene prioritization interface that ranks gene products for annotation.
Indeed, the identification of iso-orthologs should represent an important component of genome annotation strategies, comparative studies, phylogenetic analyses and functional genomics approaches, particularly given the fact that splicing variants can be lost or acquired in a taxon-specific manner during the evolutionary process.
The M1 module, which requires very high levels of similarity, is typically the most effective Sma3s component for annotation of these sequences (Supplementary Fig. S1b).
One of the basic components of the annotation of any genome is an accurate representation of protein-coding genes.
The various components of this annotation tool include the Development of Common Data Elements (CDEs) that are derived from College of American Pathologists CAPP) Checklist and North American Association of Central Cancer Registries (NAACR) standards.
While most components of the annotation pipeline were run on individual sequences, ortholog/paralog analyses were performed across species using OrthoMCL (30).
In addition to implementing and integrating components of the annotation system, we have performed computational analyses to create gene evidence tracks and a consensus gene set, which can be viewed on individual gene pages at BGD.
Components of the annotation process included Blast analyses against several databases (e.g., UniProt, Ensembl D. melanogaster-specific and An. gambiae-specific databases, Le. major genome (v4.0), an in-house "all bacterial DNA sequences" database), followed by Interpro scans of the predicted Lutzomyia proteins to identify motifs/domains.
These results further our understanding of the evolutionary fates of duplicate genes following allopolyploidization. Information on key evolutionary events (such as duplications), as well as rates and patterns of evolutionary change, are an important component of the functional annotation of genes and genomes [ 91].
The distribution of annotated unigenes under different GO levels of each category shows a concentration in 4-7, 3-7 and 4-7 levels respectively for biological process, molecular function, and cellular component, indicating a good accuracy of annotation.
