Infernal

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Description

Infernal is used to search sequence databases for homologs of structural RNA sequences, and to make sequence- and structure-based RNA sequence alignments. Infernal builds a profile from a structurally annotated multiple sequence alignment of an RNA family with a position-specific scoring system for substi- tutions, insertions, and deletions. Positions in the profile that are basepaired in the consensus secondary structure of the alignment are modeled as dependent on one another, allowing Infernal’s scoring system to consider the secondary structure, in addition to the primary sequence, of the family being modeled. Infernal profiles are probabilistic models called “covariance models”, a specialized type of stochastic context-free grammar (SCFG) (Lari and Young, 1990).

Availability

Version 1.1 Freely available for every user. Available modules:

infernal-1.1-intel
infernal-1.1-pgi
infernal-1.1-gcc

Licence

Infernal is licensed and freely distributed under the GNU General Public License version 3 (GPLv3). For a copy of the License, see GENERAL PUBLIC LICENSE.

Use

Initialize module with command:

module add infernal-1.1-intel

Program manager

meta@cesnet.cz

Homepage

http://infernal.janelia.org/