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Find unique sequence within
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18 months ago

How to find a unique sequence in within a sequence and compare it with other databases? I don't know if that sounds correct but I am new in this field >.<. Anyways, I have been given files which contains sequences and I have been asked to find a sequence which is unique to that particular gene itself. How to do that? Help me please!

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We need more information:

  • How long are the sequences?
  • How long should the minimum unique sequence be?
  • How many sequences are there?
  • Are you only trying to find unique subsequences within your data, or within all existing databases?
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This is what the collaborators want: Given that we lack the expertise to determine the necessary information from the full genome of the targets you provided us with (>900 lines of genetic code), what we would like to kindly request is to provide us with the following information:

-> a list of 6 the most prevalent target genes of interest found in your samples (3 each for Ciprofloxacin and Triclosan respectively)

-> per target gene of the above, a 15-20 base long unique sequence(s) with at least 2 mismatch bases

-> the bacterial species that correlate to these genes (1 or more?) and how unique is the above sequence (ie. is it species dependent?)

Thanks in advance!

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Do you already have the sequences of the target genes of interest? Can you share the data?

Does the sequence need to be unique within the gene, or within the whole genome?

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No I don't have the sequences of the target genes of interest. I think they won't allow me to share the data. The sequences need to be unique within the gene . Thanks for replying, I thought you lost interest in my query. :(

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This is a slightly complex problem, and we really need some at least dummy data, and an example of ideal output to help you. I can’t say that I fully understand the requirements at present.

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