1
$\begingroup$

What is the difference between lower case and upper case nucleotides in a sequence? My other question is what are the dots at the end of the sequence? Some examples are shown below:

  • GGgG,GGgG,GGgG,GGgG,GGGG,GGGG…
  • GGGG,GGGG,GGGG,GGGG,GGGG,GGGG…
  • GGGG,gggg,GGGG,GGGG,UUUU
  • ggGg,ggGg,ggGg,GGgG,GGgG,GGgG…

These sequences are real experimental samples. I obtained them from QuadBase. Here is the link below:

https://quadbase.igib.res.in/

Hopefully you will provide some literature within the thread in order to understand this concept in bioinformatics. BTW I'm a beginner in this field and hopefully this Bioinformatics Stack Exchange site will help me find out the answers.

Improve this question
$\endgroup$
1
  • 1
    $\begingroup$ Please edit your question and tell us exactly how you got these sequences. You have linked to a page with various tools, which one gave you this output? What was your input? The meaning of upper vs lower case can vary enormously depending on context. for example, in genomic sequences, lowercase letters often mean low complexity regions, but we need to know more about these specific sequences and how you got them to be able to help you. Have you looked at the quadbase paper? nar.oxfordjournals.org/content/early/2016/05/16/nar.gkw425.full $\endgroup$
    – terdon ♦
    Aug 25, 2022 at 12:24

1 Answer 1

Reset to default
0
$\begingroup$
  • GGGG,gggg,GGGG,GGGG,UUUU

Quadbase appears to be about DNA secondary structures, albeit the above example is RNA. The website states,

G-Quadruplexes or G4s are secondary DNA structures that are now established to have functionally crucial roles in various cellular processes.

Two guesses, firstly its all just a bit weird, secondly its a representation of hypoxanthine. Its more likely to be the second guess than the first.

  1. The nomenclature is a bit weird: gggg with UUUU would infer non-canonical binding/bounding in WUSS (Washington University Secondary Structure) format for a psuedoknot (type of secondary structure). If that wasn't the interpretation it would be kinda weird to share nomenclature with a major secondary structure format (WUSS) for secondary structure notation.

The 'dots', i.e. '.' appear to represent continuation, although in dot-bracket format (secondary structure format) this represents a nucleotide that doesn't hybridise.

  1. Its worth reading the paper for hypoxanthine representation (normally its 'I'), because 'I' will behave like a guanine residue and would then make sense if it was being represented as 'g'. Thus, the following means no hypoxanthine,
  • GGGG,GGGG,GGGG,GGGG,GGGG,GGGG…

My bet is its point 2, otherwise it doesn't make sense.

Improve this answer
$\endgroup$

Your Answer

By clicking “Post Your Answer”, you agree to our terms of service and acknowledge that you have read and understand our privacy policy and code of conduct.

Not the answer you're looking for? Browse other questions tagged or ask your own question.