Infernal 1.1: 100-fold faster RNA homology searches

By Eric P. Nawrocki, Sean R. Eddy. 2013

3,202 citations recorded by the source corpus.

Summary: 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. Infernal uses CMs to search for new family members in sequence databases and to create potentially large multiple sequence alignments. 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. This enables ∼100-fold acceleration over the previous version and ∼10 000-fold acceleration over exhaustive non-filtered CM searches. Availability: Source code, documentation and the benchmark are 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. Documentation includes a user’s guide with a tutorial, a discussion of file formats and user options and additional details on methods implemented in the software. Contact: nawrockie@janelia.hhmi.org

Subfields: Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Molecular Biology

Citations in the corpus

RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools (2019, methodology): “The tools help to perform searches us-ing both Blast (50) on the PDB database and Infernal (51) on the Rfam database (52).”
Plant intraspecific variation modulates nutrient cycling through its below ground rhizospheric microbiome (2019, methodology): “The reconstruction of phylogenetic relationships in bacterial taxa was made for 2,650 bacterial OTUs, that were aligned with INFERNAL (Nawrocki & Eddy, 2013), by using RAxML 7.3.0 (Stamatakis, 2006) (Material and Methods S1).”
MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization (2019, background): “1 (36) with the published rRNA CMs based on alignments that were extensively manually curated (31).”
Rfam 13.0: shifting to a genome-centric resource for non-coding RNA families (2017, methodology): “Rfam uses the Infernal software package (3) to build CMs and perform iterative sequenceand secondary structure-based searches against a sequence database to find other instances of the family.”
3D RNA and Functional Interactions from Evolutionary Couplings. (2015, positive): “To compute dss, we used the consensus secondary-structure provided by RFAM, which is inferred using a profile stochastic context-free grammar (Nawrocki and Eddy, 2013).”
25 years of serving the community with ribosomal RNA gene reference databases and tools. (2017, methodology): “RDP uses the INFERNAL tool to align all rDNA sequences (Nawrocki and Eddy, 2013).”
RNA tertiary structure prediction in CASP15 by the GeneSilico group: Folding simulations based on statistical potentials and spatial restraints (2023, methodology): “MeSSPredRNA also incorporates an Infernal scan of RNA families in the Rfam database, 5,6 and mapping of secondary structures of the homologous families on the query RNA sequence.”
NCBI prokaryotic genome annotation pipeline (2016, methodology): “Genes of ribosomal RNAs were predicted either by the BLASTn sequence similarity search using the entries from the RNA sequence database as queries or by running specialized tools, such as Infernal (5,6) and Rfam (7).”
MODOMICS: a database of RNA modifications and related information. 2023 update (2023, methodology): “‘Unmodified’ versions of sequences from MODOMICS were aligned to covariance models from Rfam ( 23 ) using Infernal ( 24 ).”
3dRNA v2.0: An Updated Web Server for RNA 3D Structure Prediction (2019, methodology): “In order to get the multiple sequence alignment from the target sequence, the Infernal package [40] is used.”