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I have many alignments from Rfam Database, and I would like to edit them. I saw that many tools are used for Protein sequence alignments, but there is something specific to edit RNA alignments ?

e.g. Stockholm Alignment of Pistol (just few entries).

FP929053.1/1669026-1668956   AGUGGUCACAGCCACUAUAAACA-GGGCUU-UAAGCUGUG-AGCGUUGACCGUC----------ACAA-----CGGCGGUCAGGUAGUC
AFOX01000025.1/1981-1912     ACUCGUCUGAGCGAGUAUAAACA-GGUCAU-UAAGCUCAG-AGCGUUCACCGGG----------AUCA------UUCGGUGAGGUUGGC
HE577054.1/3246821-3246752   ACUCGUCUGAGCGAGUAUAAACA-GGUCAU-UAAGCUCAG-AGCGUUCACCGGG----------AUCA------UGCGGUGAGGUUGGC
CP000154.1/3364237-3364168   GUUCGUCUGAGCGAACGCAAACA-GGCCAU-UAAGCUCAG-AGCGUUCACUGGA----------UUCG------UCCAGUGAGAUUGGC`
`#=GC SS_cons                 <<<<__AAAAA_>>>>-------..<<<<-.----aaaaa.----<<<<<<<<<..........____....._>>>>>>>>>-->>>>`
`#=GC RF                      acUCGUCuggGCGAguAUAAAuA..cgCaU.UAgGCccaG.AGCGUcccggcgg..........uUau.....uccgccgggGGUuGcg
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    $\begingroup$ Is there any reason you can't use your preferred tool for editing protein alignments? The format is the same, I've never come across an alignment editor that can deal with protein but not nucleotide alignments. $\endgroup$ – terdon Jun 8 '17 at 9:19
  • $\begingroup$ Yes, because I do not have a preferred tool yet, and this question would broad my horizon of possibilities. Since it is possible that someone that use to edit RNAs has a preference between software because, maybe, one is more optimized than another. Since the bioinformatic is so vast and new tools are born every day, I don't see how this could be a stupid question. $\endgroup$ – Peter Jun 8 '17 at 10:18
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    $\begingroup$ Oh, hey, nobody said it was a stupid question! I was just asking why you specified RNA in case you needed a specific feature regarding it. In general, a sequence alignment is a sequence alignment and it doesn't make much difference if it is protein, DAN or RNA. That said, RALEE does have some RNA_specific features. $\endgroup$ – terdon Jun 8 '17 at 11:06
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I would suggest use RALEE—RNALignment Editor in Emacs. It can get for you the consensus secondary structure, you can move left/right sequences and their secondary structures (you can't do it in JalView!), and more.

It's an Emacs mode, so could be a bit hard to start off, but just try, you don't have to use all Emacs features to edit your alignments!

The RALEE (RNA ALignment Editor in Emacs) tool provides a simple environment for RNA multiple sequence alignment editing, including structure-specific colour schemes, utilizing helper applications for structure prediction and many more conventional editing functions.

Sam Griffiths-Jones Bioinformatics (2005) 21 (2): 257-259.

enter image description here

enter image description here Fig. You can move left/right sequences and their secondary structures (you can't do it in JalView!)

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    $\begingroup$ Ha! +1 for pure geekiness and for using the world's best editor! :P Are you sure about jalview not supporting such moving though? I haven't used it in a while but as I recall you could just select multiple sequences (and the structure line is just another "sequence") and any edit applied to one would be applied to all. Is that wrong? $\endgroup$ – terdon Jun 8 '17 at 9:40
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    $\begingroup$ Since I use emacs, I think this will be really good for me ! Thanks. $\endgroup$ – Peter Jun 8 '17 at 15:14
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There's nothing really special about RNA alignments, you can use any alignment editor, including whichever one you use for protein. That said, a classic and very useful tool for this sort of thing is JalView. It can be installed locally or run as a Java webapp from your browser.

Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure. The Jalview Desktop can also connect with databases and analysis services, and provides a graphical interface to the alignment and analysis services provided by the JavA Bioinformatics Analysis Web Services framework.

jalview image

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