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verified publisher icon BackofenLab

two-step approach with fast pre-filter

Open martin-raden opened this issue 6 years ago • 3 comments

Following the results and repeating the benchmark from https://doi.org/10.1093/bib/bby032 we want to test whether a combination of a fast pre-filter tool like guugle will improve IntaRNAs runtime and prediction accuracy.

  • run guugle or similar fast method to identify potential interactions
  • combine interaction ranges to predictions ranges (eg on target only)
  • run intarna on pre-filtered ranges only

martin-raden avatar Mar 04 '19 20:03 martin-raden

also check sTarPicker: A Method for Efficient Prediction of Bacterial sRNA Targets Based on a Two-Step Model for Hybridization

guugle-based with seed-extension

martin-raden avatar Apr 03 '19 07:04 martin-raden

  • ASSA https://doi.org/10.1142/S0219720018400012

martin-raden avatar Jul 15 '19 12:07 martin-raden

prefilter query sequences using its accessibility profile (precomputed or via RNAplfold or IntaRNA - filter matches based on maximal GU/AU content (check statistics on seeds of genomewide screens) - generate target region list - evaluate list features (length distribution, (estimated/modelled) time for ED computation etc) and compare to full target set

martin-raden avatar Feb 07 '23 10:02 martin-raden