Bio.codonalign 包

子模块

• Bio.codonalign.codonalignment 模块
  • CodonAlignment
    • CodonAlignment.__init__()
    • CodonAlignment.__str__()
    • CodonAlignment.__getitem__()
    • CodonAlignment.__add__()
    • CodonAlignment.get_aln_length()
    • CodonAlignment.toMultipleSeqAlignment()
    • CodonAlignment.get_dn_ds_matrix()
    • CodonAlignment.get_dn_ds_tree()
    • CodonAlignment.from_msa()
  • mktest()
• Bio.codonalign.codonseq 模块
  • CodonSeq
    • CodonSeq.__init__()
    • CodonSeq.get_codon()
    • CodonSeq.get_codon_num()
    • CodonSeq.translate()
    • CodonSeq.toSeq()
    • CodonSeq.get_full_rf_table()
    • CodonSeq.full_translate()
    • CodonSeq.ungap()
    • CodonSeq.from_seq()
    • CodonSeq.__abstractmethods__
  • cal_dn_ds()

模块内容

处理密码子比对的代码。

Bio.codonalign.build(pro_align, nucl_seqs, corr_dict=None, gap_char='-', unknown='X', codon_table=None, complete_protein=False, anchor_len=10, max_score=10)

根据蛋白质比对和相应的核苷酸构建密码子比对。

参数

• pro_align - 蛋白质 MultipleSeqAlignment 对象

• nucl_seqs - SeqIO.parse 或 SeqIO.index 返回的对象，或 SeqRecord 集合。

• corr_dict - 将蛋白质 ID 映射到核苷酸 ID 的字典

• complete_protein - 序列是否以起始密码子开头

返回一个 CodonAlignment 对象。

下面的例子回答了这个 Biostars 问题：https://www.biostars.org/p/89741/

>>> from Bio.Seq import Seq
>>> from Bio.SeqRecord import SeqRecord
>>> from Bio.Align import MultipleSeqAlignment
>>> from Bio.codonalign import build
>>> seq1 = SeqRecord(Seq('ATGTCTCGT'), id='pro1')
>>> seq2 = SeqRecord(Seq('ATGCGT'), id='pro2')
>>> pro1 = SeqRecord(Seq('MSR'), id='pro1')
>>> pro2 = SeqRecord(Seq('M-R'), id='pro2')
>>> aln = MultipleSeqAlignment([pro1, pro2])
>>> codon_aln = build(aln, [seq1, seq2])
>>> print(codon_aln)
CodonAlignment with 2 rows and 9 columns (3 codons)
ATGTCTCGT pro1
ATG---CGT pro2