Infernal 1.0: inference of RNA alignments

Nawrocki, Eric P.; Kolbe, Diana L.; Eddy, Sean R.

doi:10.1093/bioinformatics/btp157

Cited by 1,253 publications

(1,039 citation statements)

References 16 publications

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“…Ribosomal RNA genes (16S, 18S and 28S) were aligned on the basis of covariance models of secondary structure (Cannone et al ., 2002; Nawrocki et al ., 2009). For the nuclear 18S and plastid 16S genes, we used covariance models for Eukarya and Bacteria, respectively, and removed sequences shorter than 250 nucleotides in length.…”

Section: Methodsmentioning

confidence: 99%

Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta)

2018

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Summary Patterns of species richness are commonly linked to life history strategies. In diatoms, an exceptionally diverse lineage of photosynthetic heterokonts important for global photosynthesis and burial of atmospheric carbon, lineages with different locomotory and reproductive traits differ dramatically in species richness, but any potential association between life history strategy and diversification has not been tested in a phylogenetic framework.We constructed a time‐calibrated, 11‐gene, 1151‐taxon phylogeny of diatoms – the most inclusive diatom species tree to date. We used this phylogeny, together with a comprehensive inventory of first–last occurrences of Cenozoic fossil diatoms, to estimate ranges of expected species richness, diversification and its variation through time and across lineages.Diversification rates varied with life history traits. Although anisogamous lineages diversified faster than oogamous ones, this increase was restricted to a nested clade with active motility in the vegetative cells.We propose that the evolution of motility in vegetative cells, following an earlier transition from oogamy to anisogamy, facilitated outcrossing and improved utilization of habitat complexity, ultimately leading to enhanced opportunity for adaptive divergence across a variety of novel habitats. Together, these contributed to a species radiation that gave rise to the majority of present‐day diatom diversity.

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Section: Methodsmentioning

confidence: 99%

Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta)

2018

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“…A reference hok mRNA sequence derived from the Escherichia coli plasmid R1, along with the experimentally validated structure of the active transcript, were utilized to build a covariance model using the Infernal program. 20 This was used to search the complete RefSeq genomes of Gammaproteobacteria derived from NCBI Nucleotide. 21 Sequence hits that met selection criteria were mapped to the covariance model, and the alignment was extensively manually edited using the 4SALE editing program.…”

Section: Resultsmentioning

confidence: 99%

“…20 Initial alignment compilation. The covariance model based on the E. coli reference sequence and active structure was utilized to search a database consisting of all complete RefSeq genomes for Gammaproteobacteria derived from NCBI Nucleotide.…”

mentioning

confidence: 99%

ThehokmRNA family

Steif

Meyer²

2012

RNA Biology

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T he hok/sok toxin-antitoxin system of Escherichia coli plasmid R1 increases plasmid maintenance by killing plasmidfree daughter cells. The hok/sok locus specifies two RNAs: hok mRNA, which encodes a toxic transmembrane protein, and sok antisense RNA, which binds a complementary region in the hok mRNA and induces transcript degradation. During cell growth, the cis-encoded sok RNA inhibits expression of the Hok toxin. In plasmid-free segregants, the rapid decay of sok RNA relative to hok mRNA permits Hok translation, leading to cell death. This post-segregational killing mechanism relies upon the ability of the hok mRNA to adopt alternative structural configurations, which affect ease of translation and the susceptibility of the molecule to degradation. The full-length hok transcript is stable, highly structured and immune to ribosome and antisense RNA binding. Gradual 3' end processing produces dramatic structural rearrangements in the mRNA, which render the molecule translationally active and expose the sok RNA binding site. During transcription, premature ribosome and sok binding are prevented through the formation of transient metastable hairpins in the 5' end of the nascent transcript. Several hok mRNA paralogs have been identified in the genome of E. coli, and Hok protein orthologs found in the genomes of Enterobacteria. Using a combination of automated search and extensive manual editing, we compiled a multiple sequence alignment for the hok mRNA. All three experimentally validated hok mRNA structures are mapped onto this alignment, which has been submitted to the Rfam database for RNA families.

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“…This database contains more than three million sequences of both culturable and unculturable bacteria and archaea (Cole et al 2005(Cole et al , 2014. The sequences are aligned by an alignment program, called INFERNAL (INFERence of RNA ALignment), based on stochastic context that incorporates secondary structure information (Nawrocki et al 2009, Nawrocki andEddy 2013). For the taxonomic identification, this database uses the RDP Classifier tool, based on a simple Bayesian algorithm (Vilo and Dong 2012).…”

Section: Ribosomal Database Projectmentioning

confidence: 99%

“…En esta base de datos se encuentran más de tres millones de secuencias de bacterias y arqueas, tanto cultivables como no cultivables (Cole et al 2005, Cole et al 2014. Las secuencias son alineadas por medio de un programa de alineamientos basados en el contexto estocástico (INFERNAL: INFERence of RNA ALignment) que incorpora información sobre la estructura secundaria del ARNr 16S (Nawrocki et al 2009, Nawrocki y Eddy 2013. Para la identificación taxonómica, esta base de datos utiliza la herramienta RDP Classifier, la cual se basa en un algoritmo Bayesiano sencillo (Vilo y Dong 2012).…”

Section: Ribosomal Database Projectunclassified

The 16S rRNA gene in the study of marine microbial communities

et al. 2015

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ABSTRACT. New sequencing technologies and analytical capabilities have stimulated the study of microbial communities from specific environments, enabling researchers to understand the complexity of those systems. The 16S rRNA gene has proved very useful in describing the diversity and characterization of marine microbial communities, particularly of uncultivated organisms. The development of new sequencing techniques has contributed to the exponential increase in the number of reported 16S rRNA sequences as barcodes for microorganisms, forcing a review of concepts and methods for the taxonomic classification of these organisms. Manipulation and analysis of large amounts of genetic information have prompted the development of specific databases, specialized algorithms, and computational tools to compare thousands of such sequences and make a taxonomic assignment. Complete 16S rRNA sequences are thus needed for accurate and reproducible taxonomy assignment in the study of marine bacterial communities.Key words: metagenomics, marine microbial communities, 16S rRNA databases. RESUMEN. Las nuevas tecnologías de secuenciación y capacidades analíticas han estimulado el estudio de las comunidades microbianas deambientes específicos, lo cual ha permitido conocer la complejidad de estos sistemas. El gen ARNr 16S ha demostrado ser de gran utilidad para describir y caracterizar las comunidades microbianas marinas, especialmente los organismos no cultivados. Las nuevas técnicas de secuenciación han contribuido al incremento exponencial de registro de secuencias, aunque parciales, del ARNr 16S como elemento de código de barras para microorganismos. Consecuentemente, ha sido necesaria una revisión de conceptos y métodos de clasificación taxonómica para estos organismos. El manejo y análisis de una gran cantidad de información génica han impulsado el desarrollo de bases de datos específicas, algoritmos y herramientas computacionales especializadas para comparar miles de secuencias semejantes y hacer la asignación taxonómica. Por lo tanto, las secuencias completas del ARNr 16S son necesarias para una asignación taxonómica certera y reproducible en los estudios de comunidades microbianas marinas.Palabras clave: metagenómica, comunidades microbianas marinas, bases de datos ARNr 16S.

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Infernal 1.0: inference of RNA alignments

Abstract: 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.

Cited by 1,253 publications

References 16 publications

Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta)

Accelerated diversification is related to life history and locomotion in a hyperdiverse lineage of microbial eukaryotes (Diatoms, Bacillariophyta)

ThehokmRNA family

The 16S rRNA gene in the study of marine microbial communities

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