Literature DB >> 19307242

Infernal 1.0: inference of RNA alignments.

Eric P Nawrocki1, Diana L Kolbe, Sean R Eddy.   

Abstract

SUMMARY: 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 multiple sequence alignments. AVAILABILITY: Source code, documentation and benchmark downloadable from http://infernal.janelia.org. INFERNAL is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X.

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Year:  2009        PMID： 19307242      PMCID： PMC2732312          DOI： 10.1093/bioinformatics/btp157

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  15 in total

1.  Direct RNA motif definition and identification from multiple sequence alignments using secondary structure profiles.

Authors:  D Gautheret; A Lambert
Journal:  J Mol Biol       Date:  2001-11-09       Impact factor: 5.469

2.  Small subunit ribosomal RNA modeling using stochastic context-free grammars.

Authors:  M P Brown
Journal:  Proc Int Conf Intell Syst Mol Biol       Date:  2000

3.  Sequence-based heuristics for faster annotation of non-coding RNA families.

Authors:  Zasha Weinberg; Walter L Ruzzo
Journal:  Bioinformatics       Date:  2005-11-02       Impact factor: 6.937

4.  Searching genomes for noncoding RNA using FastR.

Authors:  Shaojie Zhang; Brian Haas; Eleazar Eskin; Vineet Bafna
Journal:  IEEE/ACM Trans Comput Biol Bioinform       Date:  2005 Oct-Dec       Impact factor: 3.710

5.  Homology detection via family pairwise search.

Authors:  W N Grundy
Journal:  J Comput Biol       Date:  1998       Impact factor: 1.479

Review 6.  Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

Authors:  S F Altschul; T L Madden; A A Schäffer; J Zhang; Z Zhang; W Miller; D J Lipman
Journal:  Nucleic Acids Res       Date:  1997-09-01       Impact factor: 16.971

7.  Stochastic context-free grammars for tRNA modeling.

Authors:  Y Sakakibara; M Brown; R Hughey; I S Mian; K Sjölander; R C Underwood; D Haussler
Journal:  Nucleic Acids Res       Date:  1994-11-25       Impact factor: 16.971

8.  RNA sequence analysis using covariance models.

Authors:  S R Eddy; R Durbin
Journal:  Nucleic Acids Res       Date:  1994-06-11       Impact factor: 16.971

9.  RSEARCH: finding homologs of single structured RNA sequences.

Authors:  Robert J Klein; Sean R Eddy
Journal:  BMC Bioinformatics       Date:  2003-09-22       Impact factor: 3.169

10.  A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure.

Authors:  Sean R Eddy
Journal:  BMC Bioinformatics       Date:  2002-07-02       Impact factor: 3.169
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  667 in total

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Authors:  Zhu-Hong Li; Vanina E Alvarez; Javier G De Gaudenzi; Celso Sant'Anna; Alberto C C Frasch; Juan J Cazzulo; Roberto Docampo
Journal:  J Biol Chem       Date:  2011-10-28       Impact factor: 5.157

2.  Secondary structure information does not improve OTU assignment for partial 16s rRNA sequences.

Authors:  Xiaoyu Wang; Yunpeng Cai; Yijun Sun; Rob Knight; Volker Mai
Journal:  ISME J       Date:  2011-12-15       Impact factor: 10.302

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Authors:  Mark Yandell; Daniel Ence
Journal:  Nat Rev Genet       Date:  2012-04-18       Impact factor: 53.242

Review 4.  The ubiquitous hammerhead ribozyme.

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Journal:  RNA       Date:  2012-03-27       Impact factor: 4.942

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Authors:  Laura C Bohorquez; Luisa Delgado-Serrano; Gina López; César Osorio-Forero; Vanja Klepac-Ceraj; Roberto Kolter; Howard Junca; Sandra Baena; María Mercedes Zambrano
Journal:  Microb Ecol       Date:  2011-09-27       Impact factor: 4.552

6.  RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA.

Authors:  Marie-Josée Cros; Antoine de Monte; Jérôme Mariette; Philippe Bardou; Benjamin Grenier-Boley; Daniel Gautheret; Hélène Touzet; Christine Gaspin
Journal:  RNA       Date:  2011-09-23       Impact factor: 4.942

7.  Animal snoRNAs and scaRNAs with exceptional structures.

Authors:  Manja Marz; Andreas R Gruber; Christian Höner Zu Siederdissen; Fabian Amman; Stefan Badelt; Sebastian Bartschat; Stephan H Bernhart; Wolfgang Beyer; Stephanie Kehr; Ronny Lorenz; Andrea Tanzer; Dilmurat Yusuf; Hakim Tafer; Ivo L Hofacker; Peter F Stadler
Journal:  RNA Biol       Date:  2011-11-01       Impact factor: 4.652

Review 8.  Computational analysis of riboswitch-based regulation.

Authors:  Eric I Sun; Dmitry A Rodionov
Journal:  Biochim Biophys Acta       Date:  2014-02-28

9.  MEGGASENSE - The Metagenome/Genome Annotated Sequence Natural Language Search Engine: A Platform for 
the Construction of Sequence Data Warehouses.

Authors:  Ranko Gacesa; Jurica Zucko; Solveig K Petursdottir; Elisabet Eik Gudmundsdottir; Olafur H Fridjonsson; Janko Diminic; Paul F Long; John Cullum; Daslav Hranueli; Gudmundur O Hreggvidsson; Antonio Starcevic
Journal:  Food Technol Biotechnol       Date:  2017-06       Impact factor: 3.918

10.  Identification of non-coding RNAs with a new composite feature in the Hybrid Random Forest Ensemble algorithm.

Authors:  Supatcha Lertampaiporn; Chinae Thammarongtham; Chakarida Nukoolkit; Boonserm Kaewkamnerdpong; Marasri Ruengjitchatchawalya
Journal:  Nucleic Acids Res       Date:  2014-04-25       Impact factor: 16.971
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