Infernal
Sean Eddy's suite of programs infernal,eddy2002,eddy1994 for generating covariance models (CM) from RNA alignments where a similar structure is known. These can be used by the package to search for similar structures in other sequences. The package is often used in conjunction with the Rfam database rfam for locating non-coding RNA in sequences in annotation pipelines.
The Infernal/Rfam relationship is similar in scope to Eddy's HMMER package, used in conjunction with Pfam for annotating protein sequences. In fact, CM are comparable to profile hidden Markov Models, except that secondary structural information is included along with sequence consensus information.
The Infernal package is currently nearing a final 1.0 release, with the current release at v.1.0rc1. As Infernal is still in active development, Bioperl support will likewise be experimental until the Infernal API stabilizes. At this point very little filtering is done on HSPs, so the output can be quite verbose.
A Bio::SearchIO module is available for filtering and parsing raw output from cmsearch, the Infernal program which searches sequences using a covariance model. Tools for other parsers may be added over time.
Raw Output Format (Infernal 0.72, cmsearch)
This is partial cmsearch output using a purine riboswitch covariance model.
CPU time (band calc): 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00
sequence: gi|2239287|gb|U51115.1|BSU51115
hit 0 : 15589 15691 78.40 bits
:::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60
A+ A+A+ AAAA A :CUC:UAUAAU: :GGGAAUAUGGCCC: :AGUUUCUACC:G
15589 CAUGAAAUCAAAACACGACCUCAUAUAAUCUUGGGAAUAUGGCCCAUAAGUUUCUACCCG 15648
<<<<_______>>>>>>>,,)))).))))::::::::::::::
61 gcaaCCGUAAAuugcCuGACUAcG.aGuaAauauuaaauauuu 102
GCAACCGUAAAUUGCC:GACUA:G AG: AA + ++ +++++
15649 GCAACCGUAAAUUGCCGGACUAUGcAGGGAAGUGAUCGAUAAA 15691
hit 1 : 11655 11756 81.29 bits
:::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60
A AAAU AAA+AA A+ : CGUAUAAU::CG:GAAUAUGGC:CG::AGU UCUACCA:
11655 AGAAAUCAAAUAAGAUGAAUUCGUAUAAUCGCGGGAAUAUGGCUCGCAAGUCUCUACCAA 11714
<<<<_______>>>>>>>,,))))))))::::::::::::::
61 gcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102
GC ACCGUAAAU GC:UGACUACG : AU+U +++ UUU
11715 GCUACCGUAAAUGGCUUGACUACGUAAACAUUUCUUUCGUUU 11756
Raw Output Format (Infernal 0.81, cmsearch)
CM 1: Purine
CM lambda and K undefined -- no statistics
Using CM score cutoff of 0.00
>gi|633168|emb|X83878.1|
Plus strand results:
Query = 1 - 102, Target = 168 - 267
Score = 79.36, GC = 46
:::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60
+ A A++A AA A AA:AC+C:UAUAAU::CG:G AUAUGGC:CG::AGUUUCUACC:G
168 UUACAAUAUAAUAGGAACACUCAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGG 227
<<<<_______>>>>>>>,,))))))))::::::::::::::
61 gcaaCCGUAAAuugcCuGACUAcGaGuaAauauuaaauauuu 102
CA CCGUAAA UG C:GACUA:G+GU:A A+U A+
228 GCA-CCGUAAA-UGUCCGACUAUGGGUGAGCAAUGGAACCGC 267
Minus strand results:
Query = 1 - 102, Target = 270 - 171
Score = 2.25, GC = 48
:::::::::::::::::((((((((,,,<<<<<<<_______>>>>>>>,,,,,,,,<<<
1 aAaaauaaAaaaaaaaauaCuCgUAUAaucucgggAAUAUGGcccgagaGUuUCUACCaG 60
+ + A +:AC C:UA +::: :: UA GG :: :::GU AC: G
270 CGUGCGGUUCCAUUGCUCACCCAUA-GUCGGACAU-UUACGG-UGCCCGGUAGAAACUUG 214
<<<<_______>>>>>>>,,.))))))))::::::::::::::
61 gcaaCCGUAAAuugcCuGAC.UAcGaGuaAauauuaaauauuu 102
::::CC UA ::::C : UA:G GU: + U+++AUAUU
213 CGUGCCAUAUCCACGCGAUUaUAUGAGUGUUCCUAUUAUAUUG 171
//
Fin
References
<biblio>
- infernal pmid=12520045
- rfam pmid=15608160
- eddy2002 pmid=12095421
- eddy1994 pmid=8029015
</biblio>
