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src/b/i/biopython-1.63/Bio/Align/AlignInfo.py   biopython(Download)
    alpha = Alphabet.HasStopCodon(Alphabet.Gapped(Alphabet.generic_protein, "-"), "*")
    a = Alignment(alpha)
    a.add_sequence("ID001", "MHQAIFIYQIGYP*LKSGYIQSIRSPEYDNW-")
    a.add_sequence("ID002", "MH--IFIYQIGYAYLKSGYIQSIRSPEY-NW*")
    a.add_sequence("ID003", "MHQAIFIYQIGYPYLKSGYIQSIRSPEYDNW*")

src/b/i/biopython-HEAD/Bio/Align/AlignInfo.py   biopython(Download)
    alpha = Alphabet.HasStopCodon(Alphabet.Gapped(Alphabet.generic_protein, "-"), "*")
    a = Alignment(alpha)
    a.add_sequence("ID001", "MHQAIFIYQIGYP*LKSGYIQSIRSPEYDNW-")
    a.add_sequence("ID002", "MH--IFIYQIGYAYLKSGYIQSIRSPEY-NW*")
    a.add_sequence("ID003", "MHQAIFIYQIGYPYLKSGYIQSIRSPEYDNW*")

src/b/i/biopython-1.63/Bio/FSSP/FSSPTools.py   biopython(Download)
                                   Alphabet.IUPAC.extended_protein))
    for i in sorted(mult_align_dict):
        fssp_align.add_sequence(sum_dict[i].pdb2+sum_dict[i].chain2,
                                mult_align_dict[i])
#        fssp_align._add_numbering_table()

src/b/i/biopython-1.63/Bio/Blast/Record.py   biopython(Download)
        generic = Generic.Alignment(alphabet)
        for (name, seq) in zip(seq_names, seq_parts):
            generic.add_sequence(name, seq)
 
        return generic