[Biopython] Get all alignments of a sequence against another

[Mary Kindall]

Hi Tal and Kevin,
Thanks for mail and the user friendly package. I was not aware of the
existence of "fuzzysearch" package.

Kevin, I am allowing the mismatches (to a defined maximum which is a
function of the length of the pattern) but there is a strict 'no' for
insertions and deletions.

I do see that the functions 'fuzzysearch.find_near_matches' and
'fuzzysearch.find_near_matches_with_ngrams' works perfect for mismatches.
However, I could not find a way to avoid alignment when there is an
insertion or deletion.

Is there a way to restrict the maximum distance to mismatches only?
Levenshtein distance seems to have the same issue.

Thanks and regards
Mary





On Fri, Mar 14, 2014 at 7:11 AM, Tal Einat <taleinat at gmail.com> wrote:

> On Fri, Mar 14, 2014 at 11:16 AM, Kevin Rue <kevin.rue at ucdconnect.ie>
> wrote:
> > >>> import fuzzysearch
> > >>>
> fuzzysearch.find_near_matches_with_ngram("GGGTTLTTSS","XXXXXXXXXXXXXXXXXXXGGGTTVTTSSAAAAAAAAAAAAAGGGTTLTTSSAAAAAAAAAAAAAAAAAAAAAABBBBBBBBBBBBBBBBBBBBBBBBBGGGTTLTTSS",
> >>>> 1)
>
> By the way, you should usually just use
> fuzzysearch.find_near_matches(...), which will choose an appropriate
> search method for you depending on the given parameters.
>
> - Tal Einat
>



-- 
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Mary Kindall
Yorktown Heights, NY
USA