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added 44 characters in body; edited title
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je_b
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How Stockholm format to convert the structural information of an stockholm filedot-brackets format?

I need to convert all my sequences in a Stockholm format into this:

hg19_11_6_Ala          ----------------.GG--gggaguggugu....gguuacgaaugUGGCCUCUGC-----AA.............................................................GCAGACA.........................G..CCUGGGUUCAAUU...........................
#=GR hg19_11_6_Ala  PP .................22..45677788888....899999999996777899988.....56.............................................................8999999.........................9..*************...........................

Into something like this:

 hg19_11_6_Ala         ................((..(((((((((((...)))))))))))))))))))))))....((................................)))))))))......)))).....................

Obviously, being coherent with the stockholm format. Any hint?

How to convert the structural information of an stockholm file?

I need to convert this:

hg19_11_6_Ala          ----------------.GG--gggaguggugu....gguuacgaaugUGGCCUCUGC-----AA.............................................................GCAGACA.........................G..CCUGGGUUCAAUU...........................
#=GR hg19_11_6_Ala  PP .................22..45677788888....899999999996777899988.....56.............................................................8999999.........................9..*************...........................

Into something like this:

 hg19_11_6_Ala         ................((..(((((((((((...)))))))))))))))))))))))....((................................)))))))))......)))).....................

Obviously, being coherent with the stockholm format. Any hint?

Stockholm format to dot-brackets format?

I need to convert all my sequences in a Stockholm format into this:

hg19_11_6_Ala          ----------------.GG--gggaguggugu....gguuacgaaugUGGCCUCUGC-----AA.............................................................GCAGACA.........................G..CCUGGGUUCAAUU...........................
#=GR hg19_11_6_Ala  PP .................22..45677788888....899999999996777899988.....56.............................................................8999999.........................9..*************...........................

Into something like this:

 hg19_11_6_Ala         ................((..(((((((((((...)))))))))))))))))))))))....((................................)))))))))......)))).....................

Obviously, being coherent with the stockholm format. Any hint?

edited body
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je_b
  • 211
  • 2
  • 3

I need to convert this:

hg19_11_6_Ala          ----------------.GG--gggaguggugu....gguuacgaaugUGGCCUCUGC-----AA.............................................................GCAGACA.........................G..CCUGGGUUCAAUU...........................
#=GR hg19_11_6_Ala  PP .................22..45677788888....899999999996777899988.....56.............................................................8999999.........................9..*************...........................

Into something like this:

 hg19_11_6_Ala         ................((..(((((((((((...)))))))))))))))))))))))....((................................)))))))))......)))).....................

Obviously, being coherent with the stockholm format. Any hint.?

I need to convert this:

hg19_11_6_Ala          ----------------.GG--gggaguggugu....gguuacgaaugUGGCCUCUGC-----AA.............................................................GCAGACA.........................G..CCUGGGUUCAAUU...........................
#=GR hg19_11_6_Ala  PP .................22..45677788888....899999999996777899988.....56.............................................................8999999.........................9..*************...........................

Into something like this:

 hg19_11_6_Ala         ................((..(((((((((((...)))))))))))))))))))))))....((................................)))))))))......)))).....................

Obviously, being coherent with the stockholm format. Any hint.

I need to convert this:

hg19_11_6_Ala          ----------------.GG--gggaguggugu....gguuacgaaugUGGCCUCUGC-----AA.............................................................GCAGACA.........................G..CCUGGGUUCAAUU...........................
#=GR hg19_11_6_Ala  PP .................22..45677788888....899999999996777899988.....56.............................................................8999999.........................9..*************...........................

Into something like this:

 hg19_11_6_Ala         ................((..(((((((((((...)))))))))))))))))))))))....((................................)))))))))......)))).....................

Obviously, being coherent with the stockholm format. Any hint?

Source Link
je_b
  • 211
  • 2
  • 3

How to convert the structural information of an stockholm file?

I need to convert this:

hg19_11_6_Ala          ----------------.GG--gggaguggugu....gguuacgaaugUGGCCUCUGC-----AA.............................................................GCAGACA.........................G..CCUGGGUUCAAUU...........................
#=GR hg19_11_6_Ala  PP .................22..45677788888....899999999996777899988.....56.............................................................8999999.........................9..*************...........................

Into something like this:

 hg19_11_6_Ala         ................((..(((((((((((...)))))))))))))))))))))))....((................................)))))))))......)))).....................

Obviously, being coherent with the stockholm format. Any hint.