Computational identification of noncoding RNAs in E. coli by comparative genomics.
TLDR
A computational comparative genomic screen for ncRNA genes is described, to distinguish conserved RNA secondary structures from a background of other conserved sequences using probabilistic models of expected mutational patterns in pairwise sequence alignments.About:
This article is published in Current Biology.The article was published on 2001-09-04 and is currently open access. It has received 410 citations till now. The article focuses on the topics: Noncoding DNA & Conserved non-coding sequence.read more
Citations
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lincRNAs: genomics, evolution, and mechanisms.
Igor Ulitsky,David P. Bartel +1 more
TL;DR: This Review outlines the emerging understanding of lincRNAs in vertebrate animals, with emphases on how they are being identified and current conclusions and questions regarding their genomics, evolution and mechanisms of action.
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Non-coding RNA
John S. Mattick,Igor V. Makunin +1 more
TL;DR: RNAs appear to comprise a hidden layer of internal signals that control various levels of gene expression in physiology and development, including chromatin architecture/epigenetic memory, transcription, RNA splicing, editing, translation and turnover.
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The microRNAs of Caenorhabditis elegans
Lee P. Lim,Nelson C. Lau,Earl G. Weinstein,Aliaa Abdelhakim,Soraya Yekta,Matthew W. Rhoades,Christopher B. Burge,David P. Bartel +7 more
TL;DR: The census of the worm miRNAs and their expression patterns helps define this class of noncoding RNAs, lays the groundwork for functional studies, and provides the tools for more comprehensive analyses of miRNA genes in other species.
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Non-coding RNA genes and the modern RNA world.
TL;DR: 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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A small RNA regulates the expression of genes involved in iron metabolism in Escherichia coli.
Eric Massé,Susan Gottesman +1 more
TL;DR: RyhB provides a mechanism for the cell to down-regulate iron-storage proteins and nonessential ironcontaining proteins when iron is limiting, thus modulating intracellular iron usage to supplement mechanisms for iron uptake directly regulated by Fur.
References
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Journal ArticleDOI
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.
Stephen F. Altschul,Thomas L. Madden,Alejandro A. Schäffer,Jinghui Zhang,Zheng Zhang,Webb Miller,David J. Lipman +6 more
TL;DR: A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.
Journal ArticleDOI
The Complete Genome Sequence of Escherichia coli K-12
Frederick R. Blattner,Guy Plunkett,Craig A. Bloch,Nicole T. Perna,Valerie Burland,Monica Riley,Julio Collado-Vides,Jeremy D. Glasner,Christopher K. Rode,George F. Mayhew,Jason Gregor,Nelson Wayne Davis,Heather A. Kirkpatrick,Michael A. Goeden,Debra J. Rose,Bob Mau,Ying Shao +16 more
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
Amino acid substitution matrices from protein blocks
TL;DR: This work has derived substitution matrices from about 2000 blocks of aligned sequence segments characterizing more than 500 groups of related proteins, leading to marked improvements in alignments and in searches using queries from each of the groups.
Book
Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids
TL;DR: This book gives a unified, up-to-date and self-contained account, with a Bayesian slant, of such methods, and more generally to probabilistic methods of sequence analysis.