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Input:

HARP receives the following file format (each structure in a separate file). The file must contain three lines.

  • The first containing the structure's name (no spaces or special characters are allowed).
  • The second line contains the sequence in a single continuous line (the only characters allowed are ACGTUacgtu).
  • The third line contains the structure in a single continuous line (the only characters allowed are ()[]{} and .).

    • Sample input files:

    First file:

    1u8dA
    GGACAUAUAAUCGCGUGGAUAUGGCACGCAAGUUUCUACCGGGCACCGUAAAUGUCCGACUAUGUCC
    ((((((({..(((((((.[[[.[[)))))))((...)})((((((]]()]]]))))))..)))))))

    Second file:

    1y26X
    CGCUUCAUAUAAUCCUAAUGAUAUGGUUUGGGAGUUUCUACCAAGAGCCUUAAACUCUUGAUUAUGAAGUG
    ((((((((({..(((((((.[[[.[[)))))))((...)})((((((]]..]]]))))))..)))))))))

    Output:

    HARP aligns helices of length 3 or more (i.e 3 consecutive base-pairs). The output format is a list of aligned helices. For each aligned helix the indices of it's middle base-pair are noted followed by the helix length (number of consecutive base-pairs).

    Structure1: HB1-HE1 length=L1Structure2: HB2-HE2 length=L2
  • Structure1, Structure2: names of the input structures.
  • HB1,HE1: the indices of the helix middle base-pair (HB and HE : opening base pair and ending base-pair) in Structure1.
  • HB2,HE2: as HB1,HE1for helix in Structure2.

    • Sample output file:

    #long helices in 1u8dA:4
    #long helices in 1y26X:4
    #base-pairs in long helices of 1u8dA:23
    #base-pairs in long helices of 1y26X:25
    #helices matched:4
    #base-pairs matched:23
    1u8dA:4-64length=71y26X:5-67length=9
    1u8dA:14-28length=71y26X:16-30length=7
    1u8dA:20-51length=31y26X:22-53length=3
    1u8dA:43-55length=61y26X:45-57length=6