受全球 DNA 序列比对启发的字符串比对

Question

我想做类似的事情：

library(Biostrings)
s1 <-DNAString("ACTTCACCAGCTCCCTGGCGGTAAGTTGATCAAAGGAAACGCAAAGTTTTCACTTCACCAGCTCCCTGGCGGTAAGTTGATCAAAGGAAACGCAAAGTTTTCAAGAAGACTTCACCAGCTCCCTGGCGGTAAGTTGATCAAAGGAAACGCAAAGTTTTCAAG")
s2 <-DNAString("GTTTCACTACTTCCTTTCGGGTAAGTAAATATATGTTTCACTACTTCCTTTCGGGTAAGTGTTTCACTACTTCCTTTCGGGTAAGTAAATATATAAATATATAAAAATATAATTTTCATCAAATATATAAATATATAAAAATATAATTTTCATCAAATATATAAAAATATAATTTTCATC")
pairwiseAlignment(s1,s2)

但使用这样的字符串：

x123 x4531 等

而不是 DNA 字母字符。有没有人知道在 R 甚至 Python 中实现此目的的软件包。谢谢！

Answer 1

Biopython's Align 模块可以接受您选择的字母表，例如

>>> from Bio import Align
>>> aligner = Align.PairwiseAligner()
>>> aligner.mode = "global"
>>> aligner.alphabet
'ABCDEFGHIJKLMNOPQRSTUVWXYZ'
>>> aligner.alphabet += "1234567890"
>>> alignments = aligner.align("X123Y", "B12XYXYXYX")
>>> print(alignments[0])
X-123-Y-----
--||--|-----
-B12-XYXYXYX

受全球 DNA 序列比对启发的字符串比对

string alignment inspired by global DNA sequence allignment

python

r

bioconductor