Apollo: a sequence annotation editor

Abstract

The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting each annotation. Apollo was developed to meet this need, enabling curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome and it is increasingly being used as a starting point for the development of customized annotation editing tools for other genome projects. RationaleUnadorned genomic sequence data is simply a string of As, Ts, Gs, and Cs, with perhaps an associated confidence value for each base. In this raw state, sequence data provides very little biological insight. To utilize any sequence it must be interpreted in the context of other biological knowledge. This is the process of annotation, the task of adding explanatory notations to the sequence text. We define an annotation as the biological evaluation and explanation of a specific region on a nucleic acid sequence that includes, but is not limited to, gene transcripts. Any feature that can be anchored to the sequence -for example, an exon, a promoter, a transposable element, a regulatory region, or a CpG island -is an annotation. The genomic sequence will stabilize and reach a finite endpoint, but the annotations will continue to evolve indefinitely, as biological knowledge increases. To understand the genetic legacy of an organism we must interpret its genomic sequence, translating the information it contains in molecular form into humanreadable annotations.Part of this process is purely computational, and in its simplest terms can be described as a process of recognition: can anything be located that is somehow already familiar? The first obvious tactic is to collect sequences that may represent interesting biological features and to search the genomic sequence in order to discover the presence or absence of similar sequences. The principle is the same whether the sequences used in this comparison are expressed sequence tags (ESTs), full-length cDNAs, repeated elements or highly conserved sequences, and whether the sequences come from the same species, a closely related species or a distantly

A computational and experimental approach to validating annotations and gene predictions in theDrosophila melanogastergenome

“…Matches were filtered by using the BERKELEY OUTPUT PARSER (11). The control, GENSCAN, FGENESH, and Heidelberg (2) predictions and associated oligos were loaded into a modified release 3.1 gadfly database, and each prediction was visualized with aligned RT-PCR products and oligos by using the APOLLO genome annotation browser and editor (15). In some cases, poor RT-PCR product sequence quality required manual National Center for Biotechnology Information BLASTN (16) comparison against the release 3 genomic sequence.…”

The genome of the leaf-cutting antAcromyrmex echinatiorsuggests key adaptations to advanced social life and fungus farming

“…All gene models were subsequently filtered for transposable elements (TEs) by running InterProSscan (Zdobnov and Apweiler 2001) (see also below) while removing genes matching TE-related protein domains. Manual checking of gene models was then performed using the Apollo Annotation editor (Lewis et al 2002).…”

RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA

“…The alignment is built with ClustalW (Larkin et al 2007), and the common structure is derived with RNAz (Washietl et al 2005). It is also possible to map and visualize a selection of predictions in ApolloRNA (http://carlit.toulouse.inra.fr/ApolloRNA), an extension of the annotation environment Apollo (Lewis et al 2002) dedicated to RNA analysis. Last, selected predictions can be exported under the formats multifasta, gff, RNAML, and CSV.…”