Results 1 - 10 of 22,638

miRBase: integrating microRNA annotation and deep-sequencing data

by Ana Kozomara, Sam Griffiths-jones - Nucleic Acids Res , 2011
"... data ..."
Abstract - Cited by 545 (11 self) - Add to MetaCart
Abstract not found

The Vienna RNA Secondary Structure Server

by Ivo L. Hofacker - Nucleic Acids Res , 2003
"... The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently o#ers prediction of secondary structure from a single sequence, prediction of the consensus secondary ..."
Abstract - Cited by 611 (23 self) - Add to MetaCart
The Vienna RNA secondary structure server provides a web interface to the most frequently used functions of the Vienna RNA software package for the analysis of RNA secondary structures. It currently o#ers prediction of secondary structure from a single sequence, prediction of the consensus

Fast Folding and Comparison of RNA Secondary Structures (The Vienna RNA Package)

by Ivo L. Hofacker, Walter Fontana, Peter F. Stadler, L. Sebastian Bonhoeffer, Manfred Tacker, Peter Schuster
"... Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions and bas ..."
Abstract - Cited by 809 (117 self) - Add to MetaCart
Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures with minimum free energies as well as at computations of the equilibrium partition functions

Sequence Logos: A New Way to Display Consensus Sequences

by homas D. Schneider, Thomas D. Schneider, R. Michael Stephens - Nucleic Acids Res , 1990
"... INTRODUCTION A logo is "a single piece of type bearing two or more usually separate elements" [1]. In this paper, we use logos to display aligned sets of sequences. Sequence logos concentrate the following information into a single graphic [2]: 1. The general consensus of the sequences. ..."
Abstract - Cited by 650 (28 self) - Add to MetaCart
. The relative frequencies of every residue at every position. 4. The amount of information present at every position in the sequence, measured in bits. 5. An initiation point, cut point, or other significant location (if appropriate) . Any aligned set of DNA, RNA or protein sequences can be represented using

Alternative isoform regulation in human tissue transcriptomes

by Eric T. Wang, Rickard S, Shujun Luo, Irina Khrebtukova, Lu Zhang, Christine Mayr, Stephen F. Kingsmore, Gary P. Schroth, Christopher B. Burge - Nature , 2008
"... Through alternative processing of pre-mRNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes based on deep sequencing of ..."
Abstract - Cited by 545 (6 self) - Add to MetaCart
Through alternative processing of pre-mRNAs, individual mammalian genes often produce multiple mRNA and protein isoforms that may have related, distinct or even opposing functions. Here we report an in-depth analysis of 15 diverse human tissue and cell line transcriptomes based on deep sequencing

Mfold web server for nucleic acid folding and hybridization prediction

by Michael Zuker - Nucleic Acids Res , 2003
"... The abbreviated name,‘mfold web server’,describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding ..."
Abstract - Cited by 1992 (0 self) - Add to MetaCart
The abbreviated name,‘mfold web server’,describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding

A mammalian microRNA expression atlas based on small RNA library sequencing.

by Pablo Landgraf , Mirabela Rusu , Robert Sheridan , Alain Sewer , Nicola Iovino , Alexei Aravin , Sé Bastien Pfeffer , Amanda Rice , Alice O Kamphorst , Markus Landthaler , Carolina Lin , Nicholas D Socci , Leandro Hermida , Valerio Fulci , Sabina Chiaretti , Robin Foà , Julia Schliwka , Uta Fuchs , Astrid Novosel , Roman-Ulrich Mü , Bernhard Schermer , Ute Bissels , Jason Inman , Quang Phan , David B Weir , Ruchi Choksi , Gabriella De Vita , Daniela Frezzetti , Hans-Ingo Trompeter , Veit Hornung , Grace Teng , Gunther Hartmann , Miklos Palkovits , Roberto Di Lauro , Peter Wernet , Giuseppe Macino , Charles E Rogler , James W Nagle , Jingyue Ju , F Nina Papavasiliou , Thomas Benzing , Peter Lichter , Wayne Tam , Michael J Brownstein , Andreas Bosio , James J Russo , Chris Sander , Mihaela Zavolan , Thomas Tuschl - Cell, , 2007
"... SUMMARY MicroRNAs (miRNAs) are small noncoding regulatory RNAs that reduce stability and/or translation of fully or partially sequencecomplementary target mRNAs. In order to identify miRNAs and to assess their expression patterns, we sequenced over 250 small RNA libraries from 26 different organ sy ..."
Abstract - Cited by 418 (4 self) - Add to MetaCart
SUMMARY MicroRNAs (miRNAs) are small noncoding regulatory RNAs that reduce stability and/or translation of fully or partially sequencecomplementary target mRNAs. In order to identify miRNAs and to assess their expression patterns, we sequenced over 250 small RNA libraries from 26 different organ

Compilation of tRNA sequences and sequences of tRNA genes

by Mathias Sprinzl, Carsten Horn, Melissa Brown, Anatoli Ioudovitch, Sergey Steinberg - Nucleic Acids Res , 1998
"... Sequences of 3279 sequences of tRNA genes and tRNAs published up to December 1996 are included in the compilation. Alignment of the sequences, which is most compatible with the tRNA phylogeny and known threedimensional structures of tRNA, is used. Sequences and references are available under ..."
Abstract - Cited by 376 (4 self) - Add to MetaCart
Sequences of 3279 sequences of tRNA genes and tRNAs published up to December 1996 are included in the compilation. Alignment of the sequences, which is most compatible with the tRNA phylogeny and known threedimensional structures of tRNA, is used. Sequences and references are available under

miRBase: microRNA sequences, targets and gene nomenclature

by Sam Griffiths-jones, Russell J. Grocock, Stijn Van Dongen, Alex Bateman, Anton J. Enright - Nucleic Acids Res , 2006
"... nomenclature ..."
Abstract - Cited by 399 (5 self) - Add to MetaCart
nomenclature

Quartet puzzling: a quartet maximum likelihood method for reconstructing tree topologies.

by Korbinian Strimmer , Arndt Von Haeseler - Mol. Biol. Evol. , 1996
"... A versatile method, quartet puzzling, is introduced to reconstruct the topology (branching pattern) of a phylogenetic tree based on DNA or amino acid sequence data. This method applies maximum-likelihood tree reconstruction to all possible quartets that can be formed from n sequences. The quartet t ..."
Abstract - Cited by 433 (9 self) - Add to MetaCart
is always equal to or better than that of neighbor joining. For some cases with high transition/transversion bias quartet puzzling outperforms neighbor joining by a factor of 10. The application of quartet puzzling to mitochondrial RNA and tRNAVd' sequences from amniotes demonstrates the power
Results 1 - 10 of 22,638