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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    • "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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    • "The exons of the RPB1 gene are perfectly suitable for this error correction method and will provide an advantage over the rRNA gene region currently used for 454 AMF community analyses. Although the use of secondary structures of the rRNA genes as a guide for alignment is also possible [52], amino acid sequences can be more easily applied as guide for error corrections and alignments. Therefore it would be a great advantage to incorporate alignment tools such as MACSE, into the advanced pipelines for high-throughput sequencing analysis. "
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    ABSTRACT: Due to the potential of arbuscular mycorrhizal fungi (AMF, Glomeromycota) to improve plant growth and soil quality, the influence of agricultural practice on their diversity continues to be an important research question. Up to now studies of community diversity in AMF have exclusively been based on nuclear ribosomal gene regions, which in AMF show high intra-organism polymorphism, seriously complicating interpretation of these data. We designed specific PCR primers for 454 sequencing of a region of the largest subunit of RNA polymerase II gene, and established a new reference dataset comprising all major AMF lineages. This gene is known to be monomorphic within fungal isolates but shows an excellent barcode gap between species. We designed a primer set to amplify all known lineages of AMF and demonstrated its applicability in combination with high-throughput sequencing in a long-term tillage experiment. The PCR primers showed a specificity of 99.94% for glomeromycotan sequences. We found evidence of significant shifts of the AMF communities caused by soil management and showed that tillage effects on different AMF taxa are clearly more complex than previously thought. The high resolving power of high-throughput sequencing highlights the need for quantitative measurements to efficiently detect these effects.
    PLoS ONE 10/2014; 9(10). DOI:10.1371/journal.pone.0107783 · 3.23 Impact Factor
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