How to build RNA motif descriptor

Struture construction

• Hairpin:

  • h5(7,8) ss(4,5) h3

    • Restrict to helical stem of 7 to 8 and loop stem of 4 to 5

    • RNAMST may find as
      aaaaaaa cccc uuuuuuu
      <<<<<<< .... >>>>>>>

• Internal loop:

  • h5(5,6) ss(3,4) h5(7,8) ss(4,5) h3 ss(1,2) h3

    • RNAMST may find as
      aaaaa ccc aaaaaaa cccc uuuuuuu cc uuuuu
      <<<<< ... <<<<<<< .... >>>>>>> .. >>>>>

• Bulge:

  • h5(5,6) ss(3,4) h5(7,8) ss(4,5) h3 h3

    • RNAMST may find as
      aaaaa ccc aaaaaaa cccc uuuuuuu uuuuu
      <<<<< ... <<<<<<< .... >>>>>>> >>>>>

• tRNA:

  • h5(6,7) ss(2,2) h5(3,4) ss(4,11) h3 ss(1,1) h5(4,5) ss(7,7) h3 ss(4,21) h5 (4,5) ss(7,7) h3 ss(4,4) h3

    • RNAMST may find as
      aaaaaa cc aaa cccc uuu c aaaaa ccccccc uuuuu cccc
      <<<<<< .. <<< .... >>> . <<<<< ....... >>>>> ....
      aaaa ccccccc uuuu cccc uuuuuu
      <<<< ....... >>>> .... >>>>>>

Additional constraint

• mispair: only could be specified in stem

  • h5(6,8,mispair=1) ss(4,5) h3

    • the stem allow 1 mispair (include bulge) and mispair must be an internal base pair

    • RNAMST may find as
      aaaaaaa ccc uuuuuuu or aaaaaaa ccc uuu_uuu or
      <<<<<<< ... >>>>>>> or <<<.<<< ... >>>.>>> or
      aaaaaaa ccc uuuguuu or aaa_aaa ccc uuuuuuu
      <<<.<<< ... >>>.>>> or <<<.<<< ... >>>.>>>

• seq: could be specified in both of stem and loop

  • h5(6,8,seq=agcau) ss(4,5) h3

    • the stem must contain "agcau"

    • RNAMST may find as
      aagcaua ccc uaugcuu
      <<<<<<< ... >>>>>>>

  • h5(6,8,seq=^agcau) ss(4,5) h3

    • the stem must start with "agcau"

    • RNAMST may find as
      agcauaa ccc uuaugcu
      <<<<<<< ... >>>>>>>

  • h5(6,8,seq=agcau$) ss(4,5) h3

    • the stem must end with "agcau"

    • RNAMST may find as
      aaagcau ccc augcuuu
      <<<<<<< ... >>>>>>>

  • h5(5,8,seq=^agcau$) ss(4,5) h3

    • the stem must be "agcau"

    • RNAMST may find as
      agcau ccc augcu
      <<<<< ... >>>>>

  • The character in seq could be IUPAC code (see Appendix)

• mismatich: only could be specified while seq exist

  • h5(6,8,seq=agcau,mismatch=1) ss(4,5) h3

    • the stem must contain "agcau" and allow 1 mismatch

    • RNAMST may find as
      aagcuua ccc uaagcuu
      <<<<<<< ... >>>>>>>

• Appendix: IUPAC codes




Code	Description
A	Adenine
C	Cytosine
G	Guanine
T	Thymine
U	Uracil
R	Purine (A or G)
Y	Pyrimidine (C, T, or U)
M	C or A
K	T, U, or G
W	T, U, or A
S	C or G
B	C, T, U, or G (not A)
D	A, T, U, or G (not C)
H	A, T, U, or C (not G)
V	A, C, or G (not T, not U)
N	Any base (A, C, G, T, or U)