Protein fragment range format?

[abargnesi]

The fragment range description specifies the following formats:

• 5_20
  • amino-terminal fragment of unknown length
• 1_?
  • carboxyl-terminal fragment of unknown length
• ?_*
  • fragment with unknown start/stop
• ?
  fragment with unknown start/stop and a descriptor

Are these examples comprehensive? Is there an lower and upper bound when you know the start/stop positions?

/cc @ncatlett

[ncatlett]

I think you are missing part of the examples in the description. The examples are intended to be comprehensive:

• fragment with known start/stop p(HGNC:YFG, frag(5_20))
• amino-terminal fragment of unknown length p(HGNC:YFG, frag(1_?))
• carboxyl-terminal fragment of unknown length p(HGNC:YFG, frag(?_*))
• fragment with unknown start/stop p(HGNC:YFG, frag(?))
  The lower bound should be the start codon (position 1), and the upper bound is the length of the referenced protein (stop codon is represented as *)

[abargnesi]

Could we also have:

p(HGNC:YFG, frag(5_*))
(start code at position 5; unknown stop codon)

and

p(HGNC:YFG, frag(?_20))
(unknown start codon; stop codon at position 20)

[ncatlett]

yes -

• c-terminal fragment (stop at end of protein sequence) with known start - p(HGNC:YFG,frag(5_*))
• fragment with unknown start and known stop - p(HGNC:YFG, frag(?_20))

in general:

• 1 is the amino terminal end of the protein
• * is the carboxyl terminal end
• ? is an unknown/unspecified position
• any number between 1 and the length of the referenced protein can be used to specify a fragment start/stop position.