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BioExcel DNA Helical Parameters Analysis

W-17 · DNA Helical Parameters

v170 stages0 clones0

The pipeline

Every stage picks its own compute target. Temple Compute OS resolves the dependencies between them and moves the data across each boundary.

  1. 01Run Curves+ helical parameter extraction
    Consumes
    curves_config, traj, top
    Produces
    curves_lis, curves_cda
  2. 02Run Canal to generate time series and histograms
    Consumes
    canal_config, curves_cda, curves_lis
    Produces
    canal_zip, canal_rise_ser, canal_roll_ser, canal_twist_ser, canal_shift_ser, canal_slide_ser, canal_tilt_ser, canal_shear_ser, canal_stretch_ser, canal_stagger_ser, canal_buckle_ser, canal_propel_ser, canal_opening_ser, canal_inclin_ser, canal_tip_ser, canal_xdisp_ser, canal_ydisp_ser, canal_majd_ser, canal_majw_ser, canal_mind_ser, canal_minw_ser, canal_alphaC_ser, canal_alphaW_ser, canal_betaC_ser, canal_betaW_ser, canal_gammaC_ser, canal_gammaW_ser, canal_deltaC_ser, canal_deltaW_ser, canal_epsilC_ser, canal_epsilW_ser, canal_zetaC_ser, canal_zetaW_ser, canal_chiC_ser, canal_chiW_ser, canal_phaseC_ser, canal_phaseW_ser
  3. 03Average helical parameters - Rise
    Consumes
    avg_rise_config, canal_rise_ser
    Produces
    avg_rise_csv, avg_rise_jpg
  4. 04Average helical parameters - Roll
    Consumes
    avg_roll_config, canal_roll_ser
    Produces
    avg_roll_csv, avg_roll_jpg
  5. 05Average helical parameters - Twist
    Consumes
    avg_twist_config, canal_twist_ser
    Produces
    avg_twist_csv, avg_twist_jpg
  6. 06Average helical parameters - Shift
    Consumes
    avg_shift_config, canal_shift_ser
    Produces
    avg_shift_csv, avg_shift_jpg
  7. 07Average helical parameters - Slide
    Consumes
    avg_slide_config, canal_slide_ser
    Produces
    avg_slide_csv, avg_slide_jpg
  8. 08Average helical parameters - Tilt
    Consumes
    avg_tilt_config, canal_tilt_ser
    Produces
    avg_tilt_csv, avg_tilt_jpg
  9. 09Average helical parameters - Shear
    Consumes
    avg_shear_config, canal_shear_ser
    Produces
    avg_shear_csv, avg_shear_jpg
  10. 10Average helical parameters - Stretch
    Consumes
    avg_stretch_config, canal_stretch_ser
    Produces
    avg_stretch_csv, avg_stretch_jpg
  11. 11Average helical parameters - Stagger
    Consumes
    avg_stagger_config, canal_stagger_ser
    Produces
    avg_stagger_csv, avg_stagger_jpg
  12. 12Average helical parameters - Buckle
    Consumes
    avg_buckle_config, canal_buckle_ser
    Produces
    avg_buckle_csv, avg_buckle_jpg
  13. 13Average helical parameters - Propeller
    Consumes
    avg_propel_config, canal_propel_ser
    Produces
    avg_propel_csv, avg_propel_jpg
  14. 14Average helical parameters - Opening
    Consumes
    avg_opening_config, canal_opening_ser
    Produces
    avg_opening_csv, avg_opening_jpg
  15. 15Average helical parameters - Inclination
    Consumes
    avg_inclin_config, canal_inclin_ser
    Produces
    avg_inclin_csv, avg_inclin_jpg
  16. 16Average helical parameters - Tip
    Consumes
    avg_tip_config, canal_tip_ser
    Produces
    avg_tip_csv, avg_tip_jpg
  17. 17Average helical parameters - X-displacement
    Consumes
    avg_xdisp_config, canal_xdisp_ser
    Produces
    avg_xdisp_csv, avg_xdisp_jpg
  18. 18Average helical parameters - Y-displacement
    Consumes
    avg_ydisp_config, canal_ydisp_ser
    Produces
    avg_ydisp_csv, avg_ydisp_jpg
  19. 19Average helical parameters - Major Groove Depth
    Consumes
    avg_majd_config, canal_majd_ser
    Produces
    avg_majd_csv, avg_majd_jpg
  20. 20Average helical parameters - Major Groove Width
    Consumes
    avg_majw_config, canal_majw_ser
    Produces
    avg_majw_csv, avg_majw_jpg
  21. 21Average helical parameters - Minor Groove Depth
    Consumes
    avg_mind_config, canal_mind_ser
    Produces
    avg_mind_csv, avg_mind_jpg
  22. 22Average helical parameters - Minor Groove Width
    Consumes
    avg_minw_config, canal_minw_ser
    Produces
    avg_minw_csv, avg_minw_jpg
  23. 23Compute sugar puckering populations
    Consumes
    puckering_config, canal_phaseC_ser, canal_phaseW_ser
    Produces
    puckering_csv, puckering_jpg
  24. 24Compute canonical alpha/gamma backbone populations
    Consumes
    canonicalag_config, canal_alphaC_ser, canal_alphaW_ser, canal_gammaC_ser, canal_gammaW_ser
    Produces
    canonicalag_csv, canonicalag_jpg
  25. 25Compute BI/BII backbone populations
    Consumes
    bipopulations_config, canal_epsilC_ser, canal_epsilW_ser, canal_zetaC_ser, canal_zetaW_ser
    Produces
    bipopulations_csv, bipopulations_jpg
  26. 26Time series helical parameters - Rise
    Consumes
    ts_rise_config, canal_rise_ser
    Produces
    ts_rise_zip, ts_rise_CG_csv
  27. 27Time series helical parameters - Roll
    Consumes
    ts_roll_config, canal_roll_ser
    Produces
    ts_roll_zip, ts_roll_CG_csv
  28. 28Time series helical parameters - Twist
    Consumes
    ts_twist_config, canal_twist_ser
    Produces
    ts_twist_zip, ts_twist_CG_csv
  29. 29Time series helical parameters - Shift
    Consumes
    ts_shift_config, canal_shift_ser
    Produces
    ts_shift_zip, ts_shift_CG_csv
  30. 30Time series helical parameters - Slide
    Consumes
    ts_slide_config, canal_slide_ser
    Produces
    ts_slide_zip, ts_slide_CG_csv
  31. 31Time series helical parameters - Tilt
    Consumes
    ts_tilt_config, canal_tilt_ser
    Produces
    ts_tilt_zip, ts_tilt_CG_csv
  32. 32Time series helical parameters - Shear
    Consumes
    ts_shear_config, canal_shear_ser
    Produces
    ts_shear_zip, ts_shear_C_csv
  33. 33Time series helical parameters - Stretch
    Consumes
    ts_stretch_config, canal_stretch_ser
    Produces
    ts_stretch_zip, ts_stretch_C_csv
  34. 34Time series helical parameters - Stagger
    Consumes
    ts_stagger_config, canal_stagger_ser
    Produces
    ts_stagger_zip, ts_stagger_C_csv
  35. 35Time series helical parameters - Buckle
    Consumes
    ts_buckle_config, canal_buckle_ser
    Produces
    ts_buckle_zip, ts_buckle_C_csv
  36. 36Time series helical parameters - Propeller
    Consumes
    ts_propel_config, canal_propel_ser
    Produces
    ts_propel_zip, ts_propel_C_csv
  37. 37Time series helical parameters - Opening
    Consumes
    ts_opening_config, canal_opening_ser
    Produces
    ts_opening_zip, ts_opening_C_csv
  38. 38Time series helical parameters - Inclination
    Consumes
    ts_inclin_config, canal_inclin_ser
    Produces
    ts_inclin_zip
  39. 39Time series helical parameters - Tip
    Consumes
    ts_tip_config, canal_tip_ser
    Produces
    ts_tip_zip
  40. 40Time series helical parameters - X-displacement
    Consumes
    ts_xdisp_config, canal_xdisp_ser
    Produces
    ts_xdisp_zip
  41. 41Time series helical parameters - Y-displacement
    Consumes
    ts_ydisp_config, canal_ydisp_ser
    Produces
    ts_ydisp_zip
  42. 42Time series helical parameters - Major Groove Depth
    Consumes
    ts_majd_config, canal_majd_ser
    Produces
    ts_majd_zip
  43. 43Time series helical parameters - Major Groove Width
    Consumes
    ts_majw_config, canal_majw_ser
    Produces
    ts_majw_zip
  44. 44Time series helical parameters - Minor Groove Depth
    Consumes
    ts_mind_config, canal_mind_ser
    Produces
    ts_mind_zip
  45. 45Time series helical parameters - Minor Groove Width
    Consumes
    ts_minw_config, canal_minw_ser
    Produces
    ts_minw_zip
  46. 46Time series backbone torsion - alphaC
    Consumes
    ts_alphaC_config, canal_alphaC_ser
    Produces
    ts_alphaC_zip
  47. 47Time series backbone torsion - alphaW
    Consumes
    ts_alphaW_config, canal_alphaW_ser
    Produces
    ts_alphaW_zip
  48. 48Time series backbone torsion - betaC
    Consumes
    ts_betaC_config, canal_betaC_ser
    Produces
    ts_betaC_zip
  49. 49Time series backbone torsion - betaW
    Consumes
    ts_betaW_config, canal_betaW_ser
    Produces
    ts_betaW_zip
  50. 50Time series backbone torsion - gammaC
    Consumes
    ts_gammaC_config, canal_gammaC_ser
    Produces
    ts_gammaC_zip
  51. 51Time series backbone torsion - gammaW
    Consumes
    ts_gammaW_config, canal_gammaW_ser
    Produces
    ts_gammaW_zip
  52. 52Time series backbone torsion - deltaC
    Consumes
    ts_deltaC_config, canal_deltaC_ser
    Produces
    ts_deltaC_zip
  53. 53Time series backbone torsion - deltaW
    Consumes
    ts_deltaW_config, canal_deltaW_ser
    Produces
    ts_deltaW_zip
  54. 54Time series backbone torsion - epsilC
    Consumes
    ts_epsilC_config, canal_epsilC_ser
    Produces
    ts_epsilC_zip
  55. 55Time series backbone torsion - epsilW
    Consumes
    ts_epsilW_config, canal_epsilW_ser
    Produces
    ts_epsilW_zip
  56. 56Time series backbone torsion - zetaC
    Consumes
    ts_zetaC_config, canal_zetaC_ser
    Produces
    ts_zetaC_zip
  57. 57Time series backbone torsion - zetaW
    Consumes
    ts_zetaW_config, canal_zetaW_ser
    Produces
    ts_zetaW_zip
  58. 58Time series backbone torsion - chiC
    Consumes
    ts_chiC_config, canal_chiC_ser
    Produces
    ts_chiC_zip
  59. 59Time series backbone torsion - chiW
    Consumes
    ts_chiW_config, canal_chiW_ser
    Produces
    ts_chiW_zip
  60. 60Time series backbone torsion - phaseC
    Consumes
    ts_phaseC_config, canal_phaseC_ser
    Produces
    ts_phaseC_zip
  61. 61Time series backbone torsion - phaseW
    Consumes
    ts_phaseW_config, canal_phaseW_ser
    Produces
    ts_phaseW_zip
  62. 62Compute average stiffness for Twist
    Consumes
    average_stiffness_config, canal_twist_ser
    Produces
    average_stiffness_csv, average_stiffness_jpg
  63. 63Compute base-pair step stiffness matrix for CG step
    Consumes
    ts_shift_CG_csv, ts_slide_CG_csv, ts_rise_CG_csv, ts_tilt_CG_csv, ts_roll_CG_csv, ts_twist_CG_csv
    Produces
    basepair_stiffness_csv, basepair_stiffness_jpg
  64. 64Bimodality analysis of Twist at CG step
    Consumes
    dna_bimodality_config, ts_twist_CG_csv
    Produces
    bimodality_csv, bimodality_jpg
  65. 65Intra-base pair sequence correlation for Twist
    Consumes
    intraseqcorr_config, canal_twist_ser
    Produces
    intraseqcorr_csv, intraseqcorr_jpg
  66. 66Inter-base pair step sequence correlation for Twist
    Consumes
    interseqcorr_config, canal_twist_ser
    Produces
    interseqcorr_csv, interseqcorr_jpg
  67. 67Intra-base pair helical parameter correlations at C base pair
    Consumes
    ts_shear_C_csv, ts_stretch_C_csv, ts_stagger_C_csv, ts_buckle_C_csv, ts_propel_C_csv, ts_opening_C_csv
    Produces
    intrahpcorr_csv, intrahpcorr_jpg
  68. 68Inter-base pair step helical parameter correlations at CG step
    Consumes
    ts_shift_CG_csv, ts_slide_CG_csv, ts_rise_CG_csv, ts_tilt_CG_csv, ts_roll_CG_csv, ts_twist_CG_csv
    Produces
    interhpcorr_csv, interhpcorr_jpg
  69. 69Neighboring steps correlation for intra-base pair parameters
    Consumes
    intrabpcorr_config, canal_shear_ser, canal_stretch_ser, canal_stagger_ser, canal_buckle_ser, canal_propel_ser, canal_opening_ser
    Produces
    intrabpcorr_csv, intrabpcorr_jpg
  70. 70Neighboring steps correlation for inter-base pair parameters
    Consumes
    interbpcorr_config, canal_shift_ser, canal_slide_ser, canal_rise_ser, canal_tilt_ser, canal_roll_ser, canal_twist_ser
    Produces
    interbpcorr_csv, interbpcorr_jpg

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