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Infernal 1.1: 100-fold faster RNA homology searches

E. P. Nawrocki, S. R. Eddy
2013 Bioinformatics  
Version 1.1 of Infernal introduces a new filter pipeline for RNA homology search based on accelerated profile hidden Markov model (HMM) methods and HMM-banded CM alignment methods.  ...  Infernal builds probabilistic profiles of the sequence and secondary structure of an RNA family called covariance models (CMs) from structurally annotated multiple sequence alignments given as input.  ...  ACKNOWLEDGEMENTS Travis Wheeler adapted HMMER3's filters for chromosomelength sequences, and his code is integral to Infernal's pipeline.  ... 
doi:10.1093/bioinformatics/btt509 pmid:24008419 pmcid:PMC3810854 fatcat:qh2kgnrkbjdtrlx5mvcqre4yvq

tRNAscan-SE On-line: integrating search and context for analysis of transfer RNA genes

Todd M. Lowe, Patricia P. Chan
2016 Nucleic Acids Research  
High-throughput genome sequencing continues to grow the need for rapid, accurate genome annotation and tRNA genes constitute the largest family of essential, ever-present non-coding RNA genes.  ...  In this update of the tRNAscan-SE On-line resource, we tie together improvements in tRNA classification with greatly enhanced biological context via dynamically generated links between web server search  ...  ACKNOWLEDGEMENT We would like to thank Lowe Lab members Brian Lin, Allysia Mak and Aaron Cozen for their work in development of the new covariance models for tRNAscan-SE 2.0, as well as their assistance  ... 
doi:10.1093/nar/gkw413 pmid:27174935 pmcid:PMC4987944 fatcat:x4grpmkearfebiojfqyyikxmvm

Rfam: Wikipedia, clans and the "decimal" release

P. P. Gardner, J. Daub, J. Tate, B. L. Moore, I. H. Osuch, S. Griffiths-Jones, R. D. Finn, E. P. Nawrocki, D. L. Kolbe, S. R. Eddy, A. Bateman
2010 Nucleic Acids Research  
The Rfam database aims to catalogue non-coding RNAs through the use of sequence alignments and statistical profile models known as covariance models.  ...  We discuss the addition of groupings of related RNA families into clans and new developments to the website. Rfam is available on the Web at  ...  ACKNOWLEDGEMENTS Many thanks to Guy Coates, James Beal and Peter Clapham for assistance with improving the performance of computational and software infrastructure.  ... 
doi:10.1093/nar/gkq1129 pmid:21062808 pmcid:PMC3013711 fatcat:iylwci3j5vg4pf5ur3wegbcaia

Infernal 1.0: inference of RNA alignments

E. P. Nawrocki, D. L. Kolbe, S. R. Eddy
2009 Bioinformatics  
INFERNAL builds consensus RNA secondary structure profiles called covariance models (CMs), and uses them to search nucleic acid sequence databases for homologous RNAs, or to create new sequence-and structure-based  ...  Availability: Source code, documentation and benchmark downloadable from http://infernal.janelia.org.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btp157 pmid:19307242 pmcid:PMC2732312 fatcat:sa4gthfmcrhpbgr3l4vemtocti

Infernal 1.0: inference of RNA alignments

E. P. Nawrocki, D. L. Kolbe, S. R. Eddy
2009 Bioinformatics  
INFERNAL builds consensus RNA secondary structure profiles called covariance models (CMs), and uses them to search nucleic acid sequence databases for homologous RNAs, or to create new sequence-and structure-based  ...  Availability: Source code, documentation and benchmark downloadable from http://infernal.janelia.org.  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btp326 pmcid:PMC2912718 fatcat:dyxu47uo7vhohial42ijxjkvqe

fRNAdb: a platform for mining/annotating functional RNA candidates from non-coding RNA sequences

T. Kin, K. Yamada, G. Terai, H. Okida, Y. Yoshinari, Y. Ono, A. Kojima, Y. Kimura, T. Komori, K. Asai
2007 Nucleic Acids Research  
There are abundance of transcripts that code for no particular protein and that remain functionally uncharacterized.  ...  We introduce fRNAdb: a novel database service that hosts a large collection of non-coding transcripts including annotated/ non-annotated sequences from the H-inv database, NONCODE and RNAdb.  ...  ACKNOWLEDGEMENTS This research is partially supported by the Functional RNA project funded by Ministry of Economy, Trade and Industry (METI). We thank Dr. Paul Horton for his kind help.  ... 
doi:10.1093/nar/gkl837 pmid:17099231 pmcid:PMC1669753 fatcat:bpcvawirxzenxlo3cvd36smw7y

Computational identification of functional RNA homologs in metagenomic data

Eric P. Nawrocki, Sean R. Eddy
2013 RNA Biology  
models" (CMs) for rNA homology search, which harness both sequence and structural conservation when searching for rNA homologs.  ...  coding genes, structural rNAs are more difficult to identify because of their reduced alphabet size, lack of open reading frames and short length. infernal is a software package that implements "covariance  ...  . 61 Other methods exist for RNA homology search that can model RNA pseudoknots, including ERPIN 41 and RNATOPS. 45 (4) Using a CM for non-structured RNAs is pointless.  ... 
doi:10.4161/rna.25038 pmid:23722291 pmcid:PMC3849165 fatcat:zzjt2vtfxfaf7kwpup45nhebom

Rfam: updates to the RNA families database

P. P. Gardner, J. Daub, J. G. Tate, E. P. Nawrocki, D. L. Kolbe, S. Lindgreen, A. C. Wilkinson, R. D. Finn, S. Griffiths-Jones, S. R. Eddy, A. Bateman
2009 Nucleic Acids Research  
Rfam is a collection of RNA sequence families, represented by multiple sequence alignments and covariance models (CMs).  ...  The primary aim of Rfam is to annotate new members of known RNA families on nucleotide sequences, particularly complete genomes, using sensitive BLAST filters in combination with CMs.  ...  ACKNOWLEDGEMENTS We would like to thank Ivo Hofacker and Andreas Gruber for secondary structure graphics code, and Zasha Weinberg, Jeffrey Barrick, Chris Brown, Tom Jones for contributions to the database  ... 
doi:10.1093/nar/gkn766 pmid:18953034 pmcid:PMC2686503 fatcat:b2nst2s35zcrxdcepwtmmmqmmy

Fast filtering for RNA homology search

D. L. Kolbe, S. R. Eddy
2011 Bioinformatics  
Motivation: Homology search for RNAs can use secondary structure information to increase power by modeling base pairs, as in covariance models, but the resulting computational costs are high.  ...  Results: Here we present the multi-segment CYK (MSCYK) filter, which implements a heuristic of ungapped structural alignment for RNA homology search.  ...  (B) Corresponding structure for the human sequence. (C) Model construction of a CM. Fig. 2 . 2 Multi-hit ungapped consensus matches. (A) Example of non-coding RNA, from Figure 1.  ... 
doi:10.1093/bioinformatics/btr545 pmid:21965818 pmcid:PMC3208395 fatcat:xvs4dkrzunfchjwwpwoaah2h3i

A Genetic Algorithms Approach to Non-coding RNA Gene Searches

S. Smith
2006 2006 IEEE Mountain Workshop on Adaptive and Learning Systems  
A genetic algorithm is proposed as an alternative to the traditional linear programming method for scoring covariance models in non-coding RNA (ncRNA) gene searches.  ...  It is shown that a fixed-length representation for alignment of two sequences taken from the protein threading literature can be adapted for use with covariance models.  ...  ACKNOWLEDGMENT The project described was supported by NIH Grant Number P20 RR016454 from the INBRE Program of the National Center for Research Resources.  ... 
doi:10.1109/smcals.2006.250691 fatcat:tfeh6g6jr5bsdpwggng3uxle5q

Sequence and phylogenetic analysis revealed structurally conserved domains and motifs in lincRNA-p21 [article]

Aditi Maulik, Devleena Bandopadhyay, Mahavir Singh
2021 bioRxiv   pre-print
Long Intergenic Non-coding RNAs (lincRNAs) are the largest class of long non-coding RNAs in the eukaryotes, which originate from the intergenic regions of the genome.  ...  Using Infernal based covariance analysis, we have computed the secondary structures of these domains.  ...  Acknowledgements The authors also acknowledge funding for infrastructural support from the following programs  ... 
doi:10.1101/2021.03.24.436769 fatcat:xw6232fzufaz5hhatwngzyfcai

tRNAscan-SE 2.0: Improved Detection and Functional Classification of Transfer RNA Genes [article]

Patricia P Chan, Brian Y Lin, Allysia J Mak, Todd M Lowe
2019 bioRxiv   pre-print
We employ a new multi-model annotation strategy where predicted tRNAs are scored against a full set of isotype-specific covariance models.  ...  tRNAscan-SE has been widely used for whole-genome transfer RNA gene prediction for nearly two decades.  ...  Although research have been focused on protein coding genes, we hypothesized that it is possible for non-coding RNA genes transferring between organisms.  ... 
doi:10.1101/614032 fatcat:tynw5wewqvcixappadcc3tzlym

Annotating Functional RNAs in Genomes Using Infernal [chapter]

Eric P. Nawrocki
2013 Msphere  
Many of these tools utilize covariance models (CMs), statistical models of the conserved sequence and structure of an RNA family.  ...  Many different types of functional non-coding RNAs participate in a wide range of important cellular functions but the large majority of these RNAs are not routinely annotated in published genomes.  ...  Acknowledgements I thank Sean Eddy and Tom Jones for useful discussions and critical comments on the manuscript.  ... 
doi:10.1007/978-1-62703-709-9_9 pmid:24639160 fatcat:wk57ltoot5hgthxun6hwauyyri

RNA Gene Finding with Biased Mutation Operators

S.F. Smith
2007 2007 IEEE Symposium on Computational Intelligence and Bioinformatics and Computational Biology  
The use of genetic algorithms for non-coding RNA gene finding has previously been investigated and found to be a potentially viable method for accelerating covariance-model-based database search relative  ...  Since the covariance models are estimated from multiple known members of a non-coding RNA family, information is available as to the likelihood of insertions or deletions at the individual model positions  ...  ACKNOWLEDGMENT The project described was supported by NIH Grant Number P20 RR016454 from the INBRE Program of the National Center for Research Resources.  ... 
doi:10.1109/cibcb.2007.4221232 fatcat:nr6dlijigfecrad2rpqhe6nxoy

tRNAscan-SE 2.0: improved detection and functional classification of transfer RNA genes

Patricia P Chan, Brian Y Lin, Allysia J Mak, Todd M Lowe
2021 Nucleic Acids Research  
We employ a new comparative multi-model strategy where predicted tRNAs are scored against a full set of isotype-specific covariance models, allowing functional prediction based on both the anticodon and  ...  tRNAscan-SE has been widely used for transfer RNA (tRNA) gene prediction for over twenty years, developed just as the first genomes were decoded.  ...  ACKNOWLEDGEMENTS We would like to thank Aaron Cozen for his valuable feedback during the development of tRNAscan-SE 2.0.  ... 
doi:10.1093/nar/gkab688 pmid:34417604 fatcat:4vr7aufmyzecxcadi3gfax23rq
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