hello,
I'm trying to write a code to algin 2 sequences where gaps are for free in the beginning and the end of the second sequence i.e.
s1 = CATACGTCGACGGCT
s2 = ACGACGT**AAAAC**
Alignment:
CATACGTCGACGGCT
---ACGACGT-----------
I need to stop at some point(T for example) in s2 where the two sequences don't match anymore ( global alignment with free gaps at start and end)
I used a semi global alignment approach s1 in row, s2 in column , initialize the first row to 0 , initialize the 1st column as gaps accumulation
Questions :1- what is the best way to chose the beginning of trace back , is it the maximum of the last row ? 2- for this problem filling the matrix is like local alignment (minimum =0) or like the global one ore negative values are allowed ?
This looks much more like local alignment for me (no start/end gap penalty). May be this is the right algorithm for you?
local also sets all negative scores to 0. If you only want no start/end gap penalties it is semi-global
I think what you're looking for is global alignment with cost-free-ends.
You can try various strategies with this module: https://github.com/brentp/align
Here's an example script:
s1 = "CATACGTCGACGGCT"
s2 = "ACGACGTAAAAC"
from align import aligner
for method in ("global_cfe", "glocal", "local", "global"):
print "-" * len(method)
print method
print "-" * len(method)
print "\n".join(aligner(s1, s2, method=method))
print
which creates the following output:
----------
global_cfe
----------
CATACGTCG-ACGGCT
---ACGACGTAAAAC-
------
glocal
------
ACGTCG-ACGGC
ACGACGTAAAAC
-----
local
-----
ACGTCG-ACGGC
ACGACGTAAAAC
------
global
------
CATACGTCGACGGCT
ACGACGTAAAA--C-
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There's nothing bold in s2.
check the right part now