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Infernal(1)			Infernal Manual			   Infernal(1)

       Infernal	 -  sequence  analysis using profiles of RNA sequence and sec-
       ondary structure	consensus

	 Align sequences to a covariance model

	 Construct covariance model(s) from structurally annotated RNA	multi-
       ple sequence alignment(s)

	 Fit exponential tails for covariance model E-value determination

	 Convert Infernal covariance model files

	 Sample	sequences from a covariance model

	 Retrieve covariance model(s) from a file

	 Prepare a covariance model database for cmscan

	 Search	sequence(s) against a covariance model database

	 Search	covariance model(s) against a sequence database

	 summary statistics for	a covariance model file

       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
       (, 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 (, but is  designed
       specifically for	structural RNA sequence	families.  In addition to mod-
       eling 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	 prac-

       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 se-
       quence belongs to; and to automatically construct large multiple	align-
       ments  (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	impor-
       tant 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  (	  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 man-
       ageably small structural	alignment  of  a  representative  set  of  se-
       quences,	 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 sam-
       pling from a CM.	It can also generate a "consensus" sequence.

       Each program has	its own	man page.

       This is a summary man page for the entire Infernal package.  See	 indi-
       vidual  man pages [cmbuild(1), for example] for usage, options, and de-
       scription of each program in the	package.

       For complete documentation, see the user	guide that came	with your  In-
       fernal distribution (Userguide.pdf); or see the Infernal	web page ().

       Copyright (C) 2019 Howard Hughes	Medical	Institute.
       Freely distributed under	the BSD	open source license.

       For  additional	information  on	 copyright and licensing, see the file
       called COPYRIGHT	in your	Infernal source	distribution, or see  the  In-
       fernal web page ().

       Eddy/Rivas Laboratory
       Janelia Farm Research Campus
       19700 Helix Drive
       Ashburn VA 20147	USA

Infernal 1.1.3			   Nov 2019			   Infernal(1)


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