RNAs everywhere: genome‐wide annotation of structured RNAs
- 14 December 2006
- journal article
- review article
- Published by Wiley in Journal of Experimental Zoology Part B: Molecular and Developmental Evolution
- Vol. 308B (1) , 1-25
- https://doi.org/10.1002/jez.b.21130
Abstract
Starting with the discovery of microRNAs and the advent of genome‐wide transcriptomics, non‐protein‐coding transcripts have moved from a fringe topic to a central field research in molecular biology. In this contribution we review the state of the art of “computational RNomics”, i.e., the bioinformatics approaches to genome‐wide RNA annotation. Instead of rehashing results from recently published surveys in detail, we focus here ontheopen problem in the field, namely (functional) annotation of the plethora of putative RNAs. A series of exploratory studies are used to provide non‐trivial examples for the discussion of some of the difficulties.J. Exp. Zool. (Mol. Dev. Evol.) 308B, 2007.Keywords
This publication has 172 references indexed in Scilit:
- A germline-specific class of small RNAs binds mammalian Piwi proteinsNature, 2006
- A high-resolution map of transcription in the yeast genomeProceedings of the National Academy of Sciences, 2006
- Consensus Folding of Unaligned RNA Sequences RevisitedJournal of Computational Biology, 2006
- Identification of hundreds of conserved and nonconserved human microRNAsNature Genetics, 2005
- Combinatorial microRNA target predictionsNature Genetics, 2005
- Molecular Evolution of a MicroRNA ClusterPublished by Elsevier ,2004
- Prediction of Mammalian MicroRNA TargetsCell, 2003
- Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAsNature, 2002
- CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choiceNucleic Acids Research, 1994
- The equilibrium partition function and base pair binding probabilities for RNA secondary structureBiopolymers, 1990