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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 //

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
//

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.

>CR543861.1/1111804-1111620 UUGUCUCUGGG-AUGCUCGCCAGCGAGUCAGAA----UCCCC-UGA-GCCGAUACUAUCA CUUUA-----GGAUAGCGUUCUG---CAUAU-UUAGAGU-GU-AUGCCUAC--------- ------CCAGA---------GUAGGAA---AC---CCAGCAAG-U-AUG--CGUCGCU-- UCCACCUUG-----AAC----UUAA---GGGU--UCAAG--GG-------UAAUGACAGG CAGCGGCAU--CUUCGGAGGCAUU

>AB036820.1/118-302 GAGAUUAUGUA-CUCCACUCCGAUUACCUA--------GUUU-UGA--CCGAACAUUUUU UUAUAC----GGGAGCUUGCCCU--UUCCUU-UCUGCAU-AA-AUGCCCUC--------- -------AUUA---------GAGGCAC---UU---AUAAAGUC-A-GGA--AGAAAGC-A CCCACCUGC----CAUG---GUGCG---GGGU--UCA-A--AAC------GAAGGAAAGG A-GGGGAAGAAAUAAGAAAGAUAU

>AL591979.1/136531-136336 GAAACCCUAAU-GUAUUCGAUAUAGUUCCUGAU----AUUUU-UGA-ACCGAACAAUUUU UUAUACC-UAGGGAGCUUGGAGU--UCCGGC-GCGGCGC-AC-AUGCCUU---------- ------CACAC----------GAGGAA---GU---GCAAACCG-U-UAG--ACAGAGC-A CCCACCUGCU--UUAAUUGAGAGCG----GGU--UCA-A--AGG-----AAGGGAAUCCU AAACGGUAC--GAUUGGGGUUUCU

>BX842646.1/183093-182914 AGAAGGGUUCG-ACGG-CGUAAAGCUCUAUC------GAAAA-UAA-ACCUUACAAGCAU AUUUUU----GGGGACUGUCCC----UGACA-AUGGUGA-GC-AAGCUCAG--------- ------CUCGU--------ACUGAGAA---GC---CUAAAGUU-G-UUA--UCAUGGUUA CCCACCUUAG---CUAA----AACA----GGU--UUACU-UUUU-------------CAG AGUGGUCUU---CGAGCCUUUUUU

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 //