Using Apollo to Browse and Edit Genome Annotations

Sima Misra1, Nomi Harris1

1 University of California, Berkeley, California
Publication Name:  Current Protocols in Bioinformatics
Unit Number:  Unit 9.5
DOI:  10.1002/0471250953.bi0905s12
Online Posting Date:  January, 2006
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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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Table of Contents

  • 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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Materials

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Figures

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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