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Old 05-11-2019, 07:11 PM   #1
Slaanesh
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Location: Ankh Morpork

Join Date: May 2019
Posts: 1
Question Question: Finding repeats in proteins

Help!

I am looking for a software (such as Ssrtool or Tandem Repeats Finder) to help me spot motifs in my multiple (thousands) proteins, e.g.:

Code:
>seq1
nnnnnnindcndnnindcndnnindcndnnindcndnninycndnnindcndnnindcnd
nnindcndnninycndnnindcndnninycndnnindcndnnindcndnninycndnnnn
yyyyyncn
I tried searching for existing methods of analyzing such data, but I failed (all the stuff I found was for ACGT data). K-mer analysis method would not be a particularly good one because my data is highly repetitive. I also tried to use UGENE and its built-in Smith-Waterman Search plugin, but either it did not work with just one set of data and comparing it to itself, or I did something horribly wrong.

Would you happen to be able to help me find a method or software that would work with such data format? I am happy to answer any follow-up questions.
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