infernal1
Sequence analysis using profiles of rna sequence and secondary structure consensus
Usage
cmalign
Align sequences
to
a
covariance
model
cmbuild
Construct covariance
model(s)
from
structurally
annotated
RNA
multiple
sequence
alignment(s)
cmcalibrate
Fit exponential
tails
for
covariance
model
E-value
determination
cmconvert
Convert Infernal
covariance
model
files
cmemit
Sample sequences
from
a
covariance
model
cmfetch
Retrieve covariance
model(s)
from
a
file
cmpress
Prepare a
covariance
model
database
for
cmscan
cmscan
Search sequence(s)
against
a
covariance
model
database
cmsearch
Search covariance
model(s)
against
a
sequence
database
cmstat
summary statistics
for
a
covariance
model
file
Overview
Infernal is a suite of several programs for structural RNA sequence alignment and database homology search. It uses probabilistic models called "covariance models" (CMs) to represent the likely evolutionary homologs of a multiple alignment (or single sequence) of a structural RNA sequence family.
Along with the Rfam database of RNA families and associated CMs (http://rfam.sanger.ac.uk), Infernal can be used to annotate homologs of known structural RNA families in genomes.
Infernal is closely related to the HMMER software suite for sequence family analysis using profile HMMs (http://hmmer.org), but is designed specifically for structural RNA sequence families. In addition to modeling the conserved sequence of a family as profile HMMs do, CMs model the family's conserved, well-nested (non-pseudoknotted) secondary structure as well. Consequently, CM search and alignment methods are relatively computationally expensive. Infernal uses profile HMMs as filters and for deriving constraints to make the CM methods more practical.
Infernal is used in three main modes: to search a sequence database for new homologs of an RNA family (or annotate homologs in a genome); to search a CM database (like Rfam) to find what known family a query sequence belongs to; and to automatically construct large multiple alignments (i.e. with an effectively unlimited number of sequences) using a CM representative of a sequence family.
Suppose you have a structurally annotated multiple sequence alignment of a RNA sequence family of interest, and you want to search a sequence database for additional homologs. The cmbuild program builds covariance model(s) from multiple alignment(s) and cmcalibrate determines important parameters for estimating the statistical significance of database hits to the model in subsequent searches.
The cmsearch program searches CM(s) against a sequence database.
Suppose you have sequence(s) that you want to analyze using a Infernal-based CM database like Rfam (http://rfam.sanger.ac.uk). The cmpress program formats a covariance model (such as the file you would download from Rfam) into a Infernal binary database. The cmscan program searches sequence(s) against that database.
Suppose you want to align lots of sequences. You can construct a manageably small structural alignment of a representative set of sequences, build a CM with cmbuild, and use the cmalign program to align any number of sequences to that CM.
Infernal also includes some auxiliary tools for working with large CM databases. cmfetch fetches one or more CMs from a database. cmstat prints summary statistics about a CM file.
For compatibility with previous versions of Infernal, as well as with HMMER, the cmconvert program converts CM files to a few other formats.
The cmemit program generates (simulates) "homologous" sequences by sampling from a CM. It can also generate a "consensus" sequence.
Each program has its own man page.
Releases
6 releases since Debian 8 (Jessie); the text changed 3 times.