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infernal

inference of RNA secondary structural alignments

Variants:
Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.

The tool is an integral component of the Rfam database.

Homepage:
Package version:1.0.2-2
Architecture:powerpc
Distribution:Debian
Filename:infernal_1.0.2-2_powerpc.deb

/usr/share/doc/infernal/README.Debian

infernal for Debian
-------------------

The documentation for easel contains many PDFs that are not buildable
from source - although Debian most likely provide the tools at least to
prepare some of the figures, e.g., a sequence alignment.  Other figures
would be more difficult to prepare. As an interim solution it was decided
to leave that documentation out and users are requested to address the

more»

/usr/share/man/man1/cm2hmm.1.gz

cm2hmm(1)                  Infernal Manual                 cm2hmm(1)



NAME
       cm2hmm  -  build a rigorous HMM-based filter from an existing
       covariance model (CM)


SYNOPSIS
       cm2hmm cmfile hmmfile background [background parameters] HMM‐
       type optimizer [optimizer parameters]


DESCRIPTION
       cm2hmm  reads a covariance model (CM) from cmfile, constructs
       a hidden
more»

/usr/share/man/man1/cm2hmmsearch.1.gz

cmsearch(1)                Infernal Manual               cmsearch(1)



NAME
       cmsearch  - search a sequence database for RNAs homologous to
       a CM,
              using an HMM  as  a  pre-filtering  step  to  increase
              speed.


SYNOPSIS
       cmsearch  window  length  score threshold cmfile compact-type
       HMM expanded-type HMM seqfile runsearch


DESCRIPTION
       cm2
more»

/usr/share/man/man1/cmalign.1.gz

cmalign(1)                 Infernal Manual                cmalign(1)



NAME
       cmalign  -  use 
more»

/usr/share/man/man1/cmbuild.1.gz

cmbuild(1)                 Infernal Manual                cmbuild(1)



NAME
       cmbuild - constr
more»

/usr/share/man/man1/cmcalibrate.1.gz

cmcalibrate(1)             Infernal Manual            cmcalibrate(1)



NAME
       cmcalibrate  -  
more»

/usr/share/man/man1/cmemit.1.gz

cmemit(1)                  Infernal Manual                 cmemit(1)



NAME
       cmemit - generat
more»

/usr/share/man/man1/cmscore.1.gz

cmscore(1)                 Infernal Manual                cmscore(1)



NAME
       cmscore - align 
more»

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