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Information


Unique identifier OMICS_00977
Name Infernal
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Perl
Computer skills Advanced
Version 1.1.2
Stability Stable
Maintained Yes

Subtool


  • trCYK

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Documentation


Maintainer


  • person_outline Sean Eddy

Publication for Infernal

Infernal citations

 (14)
library_books

Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools

2018
Front Genet
PMCID: 5780412
PMID: 29403526
DOI: 10.3389/fgene.2017.00231

[…] ur experience in searching for riboswitches in genomes does not corroborate their report of similar searches. In our case, most of the candidate regions found while using HMMER were not identified by Infernal, and the ones that were in common were discarded according to the following threshold filters: positive values for HMMER and values above the Rfam gathering score for Infernal, or E-values gr […]

library_books

Genome Wide Detection of Small Regulatory RNAs in Deep Sea Bacterium Shewanella piezotolerans WP3

2017
Front Microbiol
PMCID: 5471319
PMID: 28663744
DOI: 10.3389/fmicb.2017.01093

[…] In present study, we extracted the IGR both from 5′ and 3′-UTR of the orthologous genes in WP3 and reference genomes and applied combination of RNAz and RNA Infernal tool to predict sRNAs in our target bacteria WP3 and four related species of Shewanella genus, i.e., S. oneidensis MR-1, S. psychrophila WP2, S. violacea DSS12, and S. benthica KT99. Positive […]

library_books

Computational identification of the selenocysteine tRNA (tRNASec) in genomes

2017
PLoS Comput Biol
PMCID: 5330540
PMID: 28192430
DOI: 10.1371/journal.pcbi.1005383

[…] s to a domain of life (archaea, bacteria and eukaryotes) and incorporates its characteristic structural features. The program scans a nucleotide sequence with the three models using cmsearch from the Infernal package (v1.1.1) []. After processing and filtering the hits by Infernal, the program produces a graphical output showing the tRNASec secondary structure (). […]

library_books

The genome, transcriptome, and proteome of the nematode Steinernema carpocapsae: evolutionary signatures of a pathogenic lifestyle

2016
Sci Rep
PMCID: 5120318
PMID: 27876851
DOI: 10.1038/srep37536

[…] Covariance models from Rfam were used to scan the genomes using Infernal software. In addition, tRNAs were predicted using tRNAscan-SE and rRNAs were predicted using RNAmmer. Finally, microRNA precursor sequences (miRNA hairpins) were located using MapMi, using al […]

library_books

An improved high quality draft genome sequence of Carnobacterium inhibens subsp. inhibens strain K1T

2016
Stand Genomic Sci
PMCID: 5016993
PMID: 27617056
DOI: 10.1186/s40793-016-0193-3

[…] uilt from SILVA []. Other non–coding RNAs such as the RNA components of the protein secretion complex and the RNase P were identified by searching the genome for the corresponding Rfam profiles using INFERNAL []. Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes platform [] developed by the Joint Genome Institute, Walnut Cree […]

library_books

High quality permanent draft genome sequence of Ensifer sp. PC2, isolated from a nitrogen fixing root nodule of the legume tree (Khejri) native to the Thar Desert of India

2016
Stand Genomic Sci
PMCID: 4918122
PMID: 27340511
DOI: 10.1186/s40793-016-0157-7

[…] uilt from SILVA []. Other non–coding RNAs such as the RNA components of the protein secretion complex and the RNase P were identified by searching the genome for the corresponding Rfam profiles using INFERNAL []. Additional gene prediction analysis and manual functional annotation was performed within the Integrated Microbial Genomes platform [] developed by the Joint Genome Institute, Walnut Cree […]

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