Apollo: a sequence annotation editor

By Suzanna Lewis, S. Searle, N. Harris, M. Gibson, V. Iyer, J. Richter, C. Wiel, L. Bayraktaroglu, Ewan Birney, Madeline A. Crosby and 9 more. Genome Biology, 2002

559 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/ae8cfc601236ee7b7667e4406423ad41f8c45087

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Citations in the corpus

The Arabidopsis Information Resource (TAIR): improved gene annotation and new tools (2011, methodology): “To maximize both efficiency and accuracy of the genome annotation process TAIR has made use of a combination of computational methods to identify genes requiring updates and carry out simpler updates, and manual curation using the Apollo gene editing tool (19) to review and carry out more complex up”
CPGView: A package for visualizing detailed chloroplast genome structures (2023, methodology): “…x s , the start position of exon 1; x e , the end position of the last exon; and d s i , the distance between i - th and ( i + 1)- th exons. the annotation results by using aPollo (version 1.11.8) software (Lewis et al., 2002) according to the multiple sequence alignment of homologous sequences.”
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review (2002, methodology): “Results and discussion We developed a set of rules for annotation to help curators using the Apollo annotation tool [19] to move quickly through the computational results for each gene, and to annotate gene models as consistently as possible (see Materials and methods).”
Creating a honey bee consensus gene set (2007, methodology): “Creating gold standard sets The Apollo annotation editor [ 15 ] was used to view all gene evidence sets simultaneously with protein homolog and EST alignments.”
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments (2007, methodology): “Manual annotation involves scientists examining all of the evidence for gene structures as described above using a graphical genome viewer and annotation editor such as Apollo [31] or Artemis [32].”
Combined Evidence Annotation of Transposable Elements in Genome Sequences (2005, methodology): “Using the Apollo annotation editor [19] to inspect these errors visually, we found that the fragmented and the nested structures of TEs often could be recovered better with these tools than in the Release 3.”
MAKER: an easy-to-use annotation pipeline designed for emerging model organism genomes. (2007, background): “There are currently more than ∼800 Eukaryotic genome projects under way (Liolios et al. 2006).”
FlyBase: genes and gene models (2004, methodology): “Annotations or larger genomic regions may also be viewed using the interactive viewing and editing tool, Apollo (19).”
A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students (2014, unknown): “Genome annotations were performed using various software platforms, including GBrowse (54), Apollo (55), DNAMaster (http://cobamide2.”
Apollo: a community resource for genome annotation editing (2009, unknown): “Contact: elee@berkeleybop.org”