Infernal 1.0: Inference of RNA alignments

HHMI Janelia Farm Research Campus, Ashburn, VA 20147, USA.
Bioinformatics (Impact Factor: 4.98). 04/2009; 25(10):1335-7. DOI: 10.1093/bioinformatics/btp157
Source: PubMed


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 infernal is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and
Mac OS/X.

Contact: nawrockie,kolbed,eddys{at}

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Available from: Eric Nawrocki, May 27, 2014
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    • "Final repeat libraries for each assembly were subsequently built using REPEATMODELER v2.1 (Smit & Hubley 2008–2010). The noncoding RNA genes were predicted with structure-based homology search by INFERNAL v1.1.1 (Nawrocki et al. 2009) against the RFAM database (Release 12.0) (Griffiths-Jones et al. 2003). We used a 'gathering' cut-off score of 85% for the covariance models and a confidence threshold (e-value) of 10 À9 . "
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    ABSTRACT: The single-humped dromedary (Camelus dromedarius), is the most numerous and widespread of domestic camel species and is a significant source of meat, milk, wool, transportation, and sport for millions of people. Dromedaries are particularly well adapted to hot, desert conditions and harbor a variety of biological and physiological characteristics with evolutionary, economic, and medical importance. To understand the genetic basis of these traits, an extensive resource of genomic variation is required. In this study, we assembled at 65x coverage, a 2.06 Gb draft genome of a female dromedary whose ancestry can be traced to an isolated population from the Canary Islands. We annotated 21,167 protein-coding genes and estimated ~33.7% of the genome to be repetitive. A comparison with the recently published draft genome of an Arabian dromedary resulted in 1.91 Gb of aligned sequence with a divergence of 0.095%. An evaluation of our genome with the reference revealed that our assembly contains more error-free bases (91.2%) and fewer scaffolding errors. We identified ~1.4 million single nucleotide polymorphisms with a mean density of 0.71 x 10(-3) per base. An analysis of demographic history indicated that changes in effective population size corresponded with recent glacial epochs. Our de novo assembly provides a useful resource of genomic variation for future studies of the camel's adaptations to arid environments and economically important traits. Furthermore, these results suggest that draft genome assemblies constructed with only two differently sized sequencing libraries can be comparable to those sequenced using additional library sizes; highlighting that additional resources might be better placed in technologies alternative to short-read sequencing to physically anchor scaffolds to genome maps. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
    Molecular Ecology Resources 07/2015; DOI:10.1111/1755-0998.12443 · 3.71 Impact Factor
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    • "Bioinformatic prediction of sRNAs in P. fluorescens SS101 genome sRNA searches were performed by BLAST and YASS (Noe and Kucherov, 2005) against the Rfam database (http://, as well as by ERPIN (Gautheret and Lambert, 2001), INFERNAL (Nawrocki et al., 2009) and DARN (Zytnicki et al., 2008), which are included in the RNASpace package (Cros et al., 2011). "
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    ABSTRACT: The rhizobacterium Pseudomonas fluorescens SS101 inhibits growth of oomycete and fungal pathogens, and induces resistance in plants against pathogens and insects. To unravel regulatory pathways of secondary metabolite production in SS101, we conducted a genome-wide search for sRNAs and performed transcriptomic analyses to identify genes associated with the Rsm (repressor of secondary metabolites) regulon. In silico analysis led to the identification of 16 putative sRNAs in the SS101 genome. In frame deletion of the sRNAs rsmY and rsmZ showed that the Rsm system regulates the biosynthesis of the lipopeptide massetolide A and involves the two repressor proteins RsmA and RsmE, with the LuxR-type transcriptional regulator MassAR as their most likely target. Transcriptome analyses of the rsmYZ mutant further revealed that genes associated with iron acquisition, motility and chemotaxis were significantly upregulated, whereas genes of the type VI secretion system were downregulated. Comparative transcriptomic analyses showed that most, but not all, of the genes controlled by RsmY/RsmZ are also controlled by the GacS/GacA two-component system. We conclude that the Rsm regulon of P. fluorescens SS101 plays a critical role in the regulation of lipopeptide biosynthesis and controls the expression of other genes involved in motility, competition and survival in the plant rhizosphere. © 2014 The Authors. Microbial Biotechnology published by John Wiley & Sons Ltd and Society for Applied Microbiology.
    Microbial Biotechnology 12/2014; 8(2). DOI:10.1111/1751-7915.12190 · 3.02 Impact Factor
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    • "23S and 5S rRNA genes within each genome were assessed manually. The rRNA gene arrangements for GenBank sequence entries containing Butyrivibrio 16S-23S rRNA regions were also examined using Infernal (Nawrocki et al. 2009) and the Rfam 11.0 database (Burge et al. 2013). "
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    ABSTRACT: The rumen is the fermentative forestomach of ruminant animals, and is host to a wide range of anaerobic bacteria whose primary function is to facilitate forage degradation. Butyrivibrio and Pseudobutyrivibrio are closely related proteolytic and fibrolytic genera within the family Lachnospiraceae, and are commonly isolated from the rumens of animals fed fibrous diets. The ribosomal RNA (rRNA) operon is an important phylogenetically informative locus that is present in multiple copies in bacterial genomes. Ribosomal RNA genes are typically arranged in the order 16S-23S-5S, with internal transcribed spacer (ITS) regions located between the genes. However, in the rumen bacterium, Butyrivibrio proteoclasticus B316, rRNA operons have a 16S-5S-23S rRNA gene arrangement, and analysis of bacterial genome projects revealed that this configuration was present in all publicly available complete genomes from members of the family Lachnospiraceae. The 16S-23S ITS region is commonly used to identify bacterial strains, thus we sought to determine the utility of this region from rumen Butyrivibrio and Pseudobutyrivibrio isolates for their rapid molecular identification. Polymerase chain reaction was used to amplify 16S-23S ITS regions, which were assessed for length polymorphism (ITS-LP), and restriction fragment length polymorphism (ITS-RFLP) using AluI, HaeIII and HhaI on a panel of 13 Butyrivibrio and Pseudobutyrivibrio reference strains. Cluster analysis of the resulting banding patterns revealed that while the ITS-LP method did not group the strains according to major Butyrivibrio and Pseudobutyrivibrio clades identified via 16S rRNA gene sequences, ITS-RFLP was more discriminative, and able to rapidly delineate the strains into these clades.
    Annals of Microbiology 12/2014; 64(4):1623-1631. DOI:10.1007/s13213-014-0806-2 · 0.99 Impact Factor
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