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Journal ArticleDOI

Non-coding RNA genes and the modern RNA world.

Sean R. Eddy
- 01 Dec 2001 - 
- Vol. 2, Iss: 12, pp 919-929
TLDR
Non-coding RNAs seem to be particularly abundant in roles that require highly specific nucleic acid recognition without complex catalysis, such as in directing post-transcriptional regulation of gene expression or in guiding RNA modifications.
Abstract
Non-coding RNA (ncRNA) genes produce functional RNA molecules rather than encoding proteins. However, almost all means of gene identification assume that genes encode proteins, so even in the era of complete genome sequences, ncRNA genes have been effectively invisible. Recently, several different systematic screens have identified a surprisingly large number of new ncRNA genes. Non-coding RNAs seem to be particularly abundant in roles that require highly specific nucleic acid recognition without complex catalysis, such as in directing post-transcriptional regulation of gene expression or in guiding RNA modifications.

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Citations
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Journal ArticleDOI

A Fiedler Vector Scoring Approach for Novel RNA Motif Selection

TL;DR: In this paper, a coarse-grained RAG (RNA-As-Graphs) framework is proposed for enumerating the universe of RNA 2D folds, selecting "RNA-like" candidates for design, and determining sequences that fold onto these candidates.
Journal ArticleDOI

Silent DNA: speaking RNA language?

TL;DR: The sequence of silent DNA in the human genome was found to have the higher thermostability of corresponding RNA/ RNA and RNA/DNA duplexes as compared with randomized sequence, suggesting that RNA-RNA and RNA-DNA interactions could be involved in the putative function of silentDNA.
Posted Content

Sequence-structure relations of biopolymers

TL;DR: In this paper, a Boltzmann sampler was used to obtain the a priori probability of specific sequence patterns in three PDB-structures, 2JXV (hairpin), 2N3R (3-branch multi-loop) and 1EHZ (tRNA).
Dissertation

Hardware accelerated genetic programming for pattern mining in strings

Pål Sætrom
TL;DR: This thesis describes a genetic programming based mining algorithm that produce state-of-the-art classifiers on two recent problems from molecular biology: i) predicting the efficacy of short interfering RNAs and antisense oligonucleotides; and ii) predicting whether or not a given DNA sequence is a non-coding RNA gene.

Development of a novel genome informatics strategy on the basis of Self-Organizing Map (SOM)

Takashi Abe
TL;DR: The modified SOM was used to analyze short oligonucleotide frequencies (dito pentanucleotide frequency) in a wide variety of prokaryotic and eukaryotic genomes and indicated that the method is useful also for survey of pathogenic microorganisms causing novel, unclear infectious diseases.
References
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Journal ArticleDOI

Initial sequencing and analysis of the human genome.

Eric S. Lander, +248 more
- 15 Feb 2001 - 
TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Journal ArticleDOI

The sequence of the human genome.

J. Craig Venter, +272 more
- 16 Feb 2001 - 
TL;DR: Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems are indicated.
Journal ArticleDOI

The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14

TL;DR: Two small lin-4 transcripts of approximately 22 and 61 nt were identified in C. elegans and found to contain sequences complementary to a repeated sequence element in the 3' untranslated region (UTR) of lin-14 mRNA, suggesting that lin- 4 regulates lin- 14 translation via an antisense RNA-RNA interaction.
Journal ArticleDOI

The Complete Genome Sequence of Escherichia coli K-12

TL;DR: The 4,639,221-base pair sequence of Escherichia coli K-12 is presented and reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident.
Journal ArticleDOI

Genetic regulatory mechanisms in the synthesis of proteins.

TL;DR: The synthesis of enzymes in bacteria follows a double genetic control, which appears to operate directly at the level of the synthesis by the gene of a shortlived intermediate, or messenger, which becomes associated with the ribosomes where protein synthesis takes place.
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Initial sequencing and analysis of the human genome.

Eric S. Lander, +248 more
- 15 Feb 2001 -