Bio.codonalign 套件

子模組

• Bio.codonalign.codonalignment 模組
  • 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 模組
  • 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()

模組內容

處理密碼子比對的程式碼。

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)

從蛋白質比對和對應的核苷酸建立密碼子比對。

引數

• pro_align - 一個蛋白質 MultipleSeqAlignment 物件

• nucl_seqs - SeqIO.parse 或 SeqIO.index 或 SeqRecord 集合所傳回的物件。

• corr_dict - 一個將蛋白質 ID 對應到核苷酸 ID 的字典

• complete_protein - 序列是否以起始密碼子開始

傳回一個 CodonAlignment 物件。

下面的範例回答了這個 Biostars 問題：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