Question: Best tool for finding short alignment between to sequences
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gravatar for juan.crescente
15 months ago by
juan.crescente20 wrote:

I have one long sequence (several kb) (I can cut it into pieces) and I want to find small parts that align (small repeats, from 10 to 500 bp long). What is the best algorithm to use? why? Preferably I want to use inside my python script.

It should allow mismatches and gaps with a penalty (maybe 1 mismatch in 10 bp, one gap).

I've tried pairwise2.align.localxx, but it gave me very long alignments as output.

alignment python • 499 views
ADD COMMENTlink modified 15 months ago by YaGalbi1.4k • written 15 months ago by juan.crescente20

To be honest this actually sounds like a motif analysis tool might do this.

For example, finding short enriched set of motif repeats in 1 long sequence....maybe try meme for this...you prob wont care for the TFs that bind, but it should find short enriched sequences in your long sequence .... then align those sequences with a multiple sequence aligner.

ADD REPLYlink modified 15 months ago • written 15 months ago by YaGalbi1.4k
0
gravatar for dariober
15 months ago by
dariober9.9k
WCIP | Glasgow | UK
dariober9.9k wrote:

blast and vmatch pop up to my mind. Both are good at finding subsequences that align between query and reference. vmatch in particular is very flexible. Since the output of vmatch is not quite in any standard format, I wrote a converter to SAM format (here).

ADD COMMENTlink written 15 months ago by dariober9.9k

the problem with BLAST is that it takes one sequence as query and one as database. I want to find small repeats / alignments between the two of thrm. I'll check vmatch

ADD REPLYlink written 15 months ago by juan.crescente20
0
gravatar for YaGalbi
15 months ago by
YaGalbi1.4k
Biocomputing, MRC Harwell Institute, Oxford, UK
YaGalbi1.4k wrote:

Plenty of tools here:

https://www.ebi.ac.uk/Tools/psa/

ADD COMMENTlink written 15 months ago by YaGalbi1.4k
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