Using Apollo to browse and edit genome annotations.
An annotation is any feature that can be tied to genomic sequence, such as an exon, transcript, promoter, or transposable element. As biological knowledge increases, annotations of different types need to be added and modified, and links to other sources of information need to be incorporated, to allow biologists to easily access all of the available sequence analysis data and design appropriate experiments. The Apollo genome browser and editor offers biologists these capabilities. Apollo can display many different types of computational evidence, such as alignments and similarities based on BLAST searches (UNITS 3.3 & 3.4), and enables biologists to utilize computational evidence to create and edit gene models and other genomic features, e.g., using experimental evidence to refine exon-intron structures predicted by gene prediction algorithms. This protocol describes simple ways to browse genome annotation data, as well as techniques for editing annotations and loading data from different sources.
Misra
Sima
S
University of California, Berkeley, California.
Harris
Nomi
N
University of California, Berkeley, California.
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods*; D003196:Computer Graphics; D003628:Database Management Systems; D030541:Databases, Genetic; D004282:Documentation / Q000379:methods*; D016247:Information Storage and Retrieval / Q000379:methods; D012984:Software; D014584:User-Computer Interface