Using Apollo to Browse and Edit Genome Annotations
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- Abstract
- Table of Contents
- Figures
- Literature Cited
Abstract
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 & ), 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.
Keywords: Genome; Sequence; Annotation; Browser; Editor
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- Basic Protocol 1: Browsing Genome Annotations in GAME XML Files
- Support Protocol 1: Editing Genome Annotations
- Support Protocol 2: Configuration Files
- Alternate Protocol 1: Browsing Genome Annotations in Chado XML Files
- Alternate Protocol 2: Browsing Genome Annotations from a Chado Database
- Alternate Protocol 3: Browsing Genome Annotations from an Ensembl Database
- Alternate Protocol 4: Browsing Genome Annotations from Ensembl GFF Files
- Alternate Protocol 5: Browsing Genome Annotations from GenBank or EMBL Files
- Commentary
- Literature Cited
- Figures
- Tables
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Figure 9.5.1 Loading an XML data file into Apollo. Drosophila annotations may also be loaded over the Internet by Gene name, Cytology, etc. by clicking on the tabs. View Image -
Figure 9.5.2 The main display of Apollo, with detail panel at the left, result panels in black, annotations panels in light blue, navigation panel at top right, and scroll and Zoom buttons at the bottom. View Image -
Figure 9.5.3 Zoomed‐in main display of Apollo, showing green start and stop codons at the top, sequence of result features, and genomic reference sequence and metric at the bottom. View Image -
Figure 9.5.4 Types panel, indicating color and presentation of each tier of data. Performing a right mouse click over a tier, in this example over Gene Prediction, brings up a pop‐up menu with the individual data types in the tier (Genscan, Genie, and FgenesH analyses). View Image -
Figure 9.5.5 Visual cues in the Apollo main display indicate new, matching, or problematic data. For example, boxed features indicate new results, white edge lines indicate matching features, cross‐hatched features have been flagged, dotted lines indicate sequencing gaps, and arrowheads indicate missing start or stop codons or nonconsensus splice sites. View Image -
Figure 9.5.6 The right‐mouse pop‐up menu (RMPM) brings up various browsing and editing functions, depending on which feature is selected. In this example, an annotated gene was selected. View Image -
Figure 9.5.7 The Annotation Info Editor in Apollo allows browsing and editing of text information, including comments, associated with annotations. View Image -
Figure 9.5.8 The Apollo Sequence window displays the sequence of selected features in FASTA format; a variety of options are available for protein‐coding gene annotations. View Image -
Figure 9.5.9 The Exon Detail Editor (EDE) allows browsing and editing of annotations while viewing the genomic sequence and three‐frame translation. Click the diagram at the bottom of the EDE to navigate within the annotated model. View Image -
Figure 9.5.10 The Jalview alignment viewer can be called from within Apollo to view multiple alignments of nucleotide and peptide sequences. View Image -
Figure 9.5.11 Part of the Chado configuration file conf/chado‐adapter.xml containing the “chadodb” element. For definitions, see Table . View Image -
Figure 9.5.12 Part of the Chado configuration file conf/chado‐adapter.xml containing the “chadoInstance” element. View Image -
Figure 9.5.13 Loading data into Apollo from an Ensembl database via the Internet. View Image -
Figure 9.5.14 Loading data into Apollo from a file in GFF format. View Image -
Figure 9.5.15 Messages printed to Java console window indicating where Apollo finds its configuration files. See for a description of the files. View Image
Videos
Literature Cited
| Burge, C. and Karlin, S. 1997. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268:78‐94. | |
| Drysdale, R.A., Crosby, M.A., Gelbart, W., Campbell, K., Emmert, D., Matthews, B., Russo, S., Schroeder, A., Smutniak, F., Zhang, P., Zhou, P., Zytkovicz, M., Ashburner, M., de Grey, A., Foulger, R., Millburn, G., Sutherland, D., Yamada, C., Kaufman, T., Matthews, K., DeAngelo, A., Cook, R.K., Gilbert, D., Goodman, J., Grumbling, G., Sheth, H., Strelets, V., Rubin, G., Gibson, M., Harris, N., Lewis, S., Misra, S., and Shu, S.Q. 2005. FlyBase: Genes and gene models. Nucl. Acids Res. 33:D390‐D395. | |
| Florea, L., Hartzell, G., Zhang, Z., Rubin, G.M., and Miller, W. 1998. A computer program for aligning a cDNA sequence with a genomic DNA sequence. Genome Res. 8:967‐974. | |
| Hubbard, T., Andrews, D., Caccamo, M., Cameron, G., Chen, Y., Clamp, M., Clarke, L., Coates, G., Cox, T., Cunningham, F., Curwen, V., Cutts, T., Down, T., Durbin, R., Fernandez‐Suarez, X.M., Gilbert, J., Hammond, M., Herrero, J., Hotz, H., Howe, K., Iyer, V., Jekosch, K., Kahari, A., Kasprzyk, A., Keefe, D., Keenan, S., Kokocinsci, F., London, D., Longden, I., McVicker, G., Melsopp, C., Meidl, P., Potter, S., Proctor, G., Rae, M., Rios, D., Schuster, M., Searle, S., Severin, J., Slater, G., Smedley, D., Smith, J., Spooner, W., Stabenau, A., Stalker, J., Storey, R., Trevanion, S., Ureta‐Vidal, A., Vogel, J., White, S., Woodwark, C., and Birney, E. 2005. Ensembl 2005. Nucl. Acids Res. 33:D447‐D453. | |
| Lewis, S.E., Searle, S.M., Harris, N., Gibson, M., Iyer, V., Richter, J., Wiel, C., Bayraktaroglu, L., Birney, E., Crosby, M.A., Kaminker, J.S., Matthews, B.B., Prochnik, S.E., Smithy, C.D., Tupy, J.L., Rubin, G.M., Misra, S., Mungall, C.J., and Clamp, M.E. 2002. Apollo: A sequence annotation editor. Genome Biol. 3:RESEARCH0082. | |
| Salamov, A.A. and Solovyev, V.V. 2000. Ab initio gene finding in Drosophila genomic DNA. Genome Res. 10:516‐522. | |
| Stein, L.D., Mungall, C., Shu, S., Caudy, M., Mangone, M., Day, A., Nickerson, E., Stajich, J.E., Harris, T.W., Arva, A., and Lewis, S. 2002. The generic genome browser: A building block for a model organism system database. Genome Res. 12:1599‐1610. | |
| Key References | |
| Lewis et al., 2002. See above. | |
| This article gives background on Apollo development and features. | |
| Internet Resources | |
| http://www.fruitfly.org/annot/apollo/ | |
| Download Apollo. | |
| http://www.fruitfly.org/annot/apollo/userguide.html | |
| Get more detailed and current information about Apollo features and usage. | |
| http://mail.fruitfly.org/mailman/listinfo/apollo | |
| Join the Apollo mailing list to ask questions or be notified of new releases. | |
| http://www.jalview.org/documentation.html | |
| Get detailed information about using Jalview, the alignment viewer in Apollo. |
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