RNA modification subsystems in the SEED database

Valérie De Crécy-Lagard, Gary Olsen

Research output: Chapter in Book/Report/Conference proceedingChapter


With over 800 genome sequences available and thousands more in the pipeline (see Genome Online Database for latest number updates1 www.genomeonline.org), the genetic information used by most biologists/biochemists is now derived mainly from genomic sequences that have been annotated in silico. Functional inferences based on comparative sequence analysis are established foundations of genomic annotation. For well studied gene families, in which the initial annotation has been experimentally verified, these homology-based methods are quite accurate in predicting function.2 However, factors such as low sequence similarity, 2 multi-domain proteins,3 gene duplications2,4 and non-orthologous displacements5 have all contributed to incorrect or absent annotations. This has been a major problem in the field of RNA modification enzymes because many are members o f large paralogous families and transferring functional annotations using BLAST scores alone can be very dangerous, particularly between kingdoms. Cases where the closest homologs in two genomes do not catalyze the same reaction are numerous in the RNA modification field with the added complication of having both tRNA and rRNA and/or snRNA as potential substrates (see refs. 6-10 for specific examples).

Original languageEnglish (US)
Title of host publicationDNA and RNA Modification Enzymes
Subtitle of host publicationStructure, Mechanism, Function and Evolution
PublisherCRC Press
Number of pages5
ISBN (Electronic)9781498713153
ISBN (Print)9781587063299
StatePublished - Jan 1 2009

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)
  • Biochemistry, Genetics and Molecular Biology(all)

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