Author: Theis, Corinna; Reeder, Jens; Giegerich, Robert
Title: KnotInFrame: prediction of -1 ribosomal frameshift events Document date: 2008_9_27
ID: 4ov0j2u3_46
Snippet: Hence, the expected run time for an average sized bacterial genome of 5 MB with 5 à 10 6  0:00195 ¼ 9750 slippery sites (and thus 9750 calls of pknotsRG-fs) is $0.6 s  9750 = 1 h 37 min. In practice, the first filter (ISF) already discards a significant amount of slippery sites (42% for the RECODE test set), before the expensive folding step and run time decreases. This effect is somehow balanced by our observation that the real genomic seq.....
Document: Hence, the expected run time for an average sized bacterial genome of 5 MB with 5 à 10 6  0:00195 ¼ 9750 slippery sites (and thus 9750 calls of pknotsRG-fs) is $0.6 s  9750 = 1 h 37 min. In practice, the first filter (ISF) already discards a significant amount of slippery sites (42% for the RECODE test set), before the expensive folding step and run time decreases. This effect is somehow balanced by our observation that the real genomic sequences used in our evaluation contain more slippery sites than expected. We measured the run time that KnotInFrame requires to analyse the 8.76 MB coding sequence of yeast. The whole computation with 43841 observed slippery sites (expected: 17109) can be performed in $4.5 CPU hours, which is a definite improvement over previous approaches.
Search related documents:
Co phrase search for related documents- cpu hour and test set: 1
- genomic sequence and test set: 1
- genomic sequence and time decrease: 1
- ISF filter and RECODE test set: 1
Co phrase search for related documents, hyperlinks ordered by date