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I try to reproduce the method of this withdrawn paper. I know this paper has been debunked and withdrawn. I am curious to understand the details of the method used on it. I am a programmer and I don't work on the field of Biology.

I have some questions about "The identified amino acid and nucleotide sequence" with MultAlign software: Image from the paper

I have trouble to understand how those supposed "inserts" were selected:

  • "Insert 1": The selection is where there are dashes and dots on the second and third lines because the sequence is not present in SARS-GZ02
  • "Insert 2": The beginning of the "insert" start with these dash and dots but why is it stopped at 155 ?
  • "Insert 3": The end at 261 is at a dash for the second line but why does it starts at 256?
  • "Insert 4": why these start and end of selection?

Later on the paper they used these selected regions with Blast and on the "motif alignement" column these letters are used which are a little different:

  • "Insert 1": TNGTKR (first letter "G" removed)
  • "Insert 2": HKNNKS ("YY" removed)
  • "Insert 3": RSYL-TPGDSSSG (4 letters at 250 added)
  • "Insert 4": QTNS-PRRA

motifs

Why are some different from the selection ?

Even for the first "insert", I can't find those alignement with Blast using for example GTNGTKR or TNGTKR. If someone could indicate me the good parameters in Blast to find these alignements it would be awesome.

Sorry if it sounds too ingenuous, thank you for your time reading all this.

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