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  • joshuapk
    Junior Member
    • Mar 2012
    • 9
    #1

    Protein Secondary Structure Guided Alignments

    So I need to make an alignment using secondary structure for gap penalties. I have found that Clustal is suppose to be able to do this but I try to follow their instructions (http://www.bugaco.com/bioinf/ClustalW/helpB.html) and it does not even read the secondary structure correctly specifically the "." are completely ignored.
    If anyone has gotten this to work for them please let me know what you did.
    Josh

    P.S. Also open to any other program that has this functionality.
    Tags: alignment, amino, clustal, gap, secondary
    • Thanh Hang
      Junior Member
      • Jul 2014
      • 2
      #2
      Hello everybody!
      I'm performing study on activity improvement of alkaline phytase in digestive tract of mono-gastric animals by site-directed mutagenesis.
      I need a software associated protein 3D structure pedict
      If anyone has gotten this to work for them please let me know what you did
      Thanks!
      p/s I known yasara, but i can't download it

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