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Infernal
Jul 20, 2023
Search sequence databases for structural RNA homologs
Infernal, standing for “INFERence of RNA ALignment”, is a tool for searching DNA sequence database for RNA structure and sequence similarities.
It is based on Covariance Model CM, which scores a combination of sequence consensus and RNA secondary structure consensus, and thus is more capable of identifying RNA homologs than using primary sequence profile.
The Rfam database of RNA families is based on Infernal.
Citation Nawrocki & Eddy 2013 Infernal 1.1 100-fold faster RNA homology searches, Bioinformatics 29 2933-2935.
Checkout these related ports:
- Wise - Intelligent algorithms for DNA searches
- Wfa2-lib - Exact gap-affine algorithm using homology to accelerate alignment
- Vt - Discovers short variants from Next Generation Sequencing data
- Vsearch - Versatile open-source tool for metagenomics
- Viennarna - Alignment tools for the structural analysis of RNA
- Velvet - Sequence assembler for very short reads
- Vcftools - Tools for working with VCF genomics files
- Vcflib - C++ library and CLI tools for parsing and manipulating VCF files
- Vcf2hap - Generate .hap file from VCF for haplohseq
- Vcf-split - Split a multi-sample VCF into single-sample VCFs
- Unikmer - Toolkit for nucleic acid k-mer analysis, set operations on k-mers
- Unanimity - Pacific Biosciences consensus library and applications
- Ugene - Integrated bioinformatics toolkit
- Ucsc-userapps - Command line tools from the UCSC Genome Browser project
- Trimmomatic - Flexible read trimming tool for Illumina NGS data