Best hits of 11110110111 : model-free selection and parameter-free sensitivity calculation of spaced seeds

This webpage provides better and extra spaced seeds: for the main datasets and scripts used in the paper, please see the original index.html before.

These results have been obtained with help of the computing power of the teaching computers of the FIL, they would probably never been obtained without the strong support provided by Mickael Carlier on BOINC.

6.bis Experiments

(a) Comparative analysis of Table 3

Before running the full parameter-free analysis (see part b), we performed, during one week, an optimization of the results provided in the table 3 of the original article, itself extracted from the rasbhari article, to test the computing capacities of the FIL BOINC cluster.

The cluster consists of about 120 to 373 (in peak) running computers (see the BOINC CPU stats). The iedera tool was run with help of the BOINC wrapper, together with an additional script layer and an add-hoc job creator/results merger adapted, usually during day hours, on already started but unused computers (jobs are stopped when a user logs in).

In this part, note that iedera performed numerical (and not symbolical) evaluations to speed up the search.

No animals (penguins, ants, ...) were harmed during this optimisation process ☺.

w	p	SpEED	AcoSeeD	FastHC	MuteHC	rasbhari	current sensitivity
SHRiMP2: 4 patterns (ℓ=50)
10	0.75	90.9098	90.9513	90.7312	92.6812	90.9614	90.9662
	0.80	97.8337	97.8521	97.7625	98.3836	97.8554	97.8559
	0.85	99.7569	99.7614	99.7431	99.8356	99.7618	99.7620
11	0.75	83.3793	83.4728	83.3068	83.4127	83.4679	83.5166
	0.80	94.9861	95.037	94.9453	95.0194	95.0386	95.0586
	0.85	99.2431	99.2478	99.2250	99.2486	99.2506	99.2573
12	0.80	90.5750	90.6328	90.4735	90.5820	90.6648	90.6672
	0.85	98.1589	98.1766	98.1199	98.1670	98.1824	98.1949
	0.90	99.8821	99.8853	99.8771	99.8836	99.8864	99.8878
16	0.85	84.8212	84.9829	84.6558	84.8764	84.969	85.0422
	0.90	97.4321	97.4712	97.3556	97.4460	97.5035	97.5337
	0.95	99.9388	99.9419	99.9347	99.9424	99.9441	99.9469
18	0.85	73.1664	73.27	72.9558		73.2209	73.4258
	0.90	93.7120	93.7778	93.6030		93.78	93.8452
	0.95	99.7500	99.7599	99.7399		99.7557	99.7664
PatternHunterII: 16 patterns (ℓ=64)
11	0.70	93.2526		93.0585		93.4653	93.4105
	0.75	98.6882		98.6352		98.7573	98.7520
	0.80	99.8820		99.8750		99.8907	99.8876
BFAST: 10 patterns (ℓ=50)
22	0.85	60.8127		60.0943		60.9919	61.0746
	0.90	88.5969		88.0426		88.8005	88.9067
	0.95	99.3659		99.2923		99.4099	99.4413

(b) Full parameter-free analysis

Please refer first to the original 6. Experiments part from main webpage and the Experiments section of the article for more details. The results are summarized on these set of plots (pdf [sep 8, 2017] or html [sep 8, 2017]). Apart form the fact that tools were run on a cluster, the main difference with the previous 6. Experiments is on the parameters used :

Seeds of weight w in [3..16] or in [18,20,22,24], span s ≤ w + 20, with a number of seed patterns n in [1..4], have been only locally optimized by the hill-climbing process of iedera,
Alignment lengths ℓ in [w+1 .. 64] have also been fully enumerated.

See the final set of Pareto plots (pdf [sep 8, 2017] or html [sep 8, 2017]), data in txt format (tar.gz [sep 8, 2017]).

Tools :

main directory : [dir]

Data & Results :

main directory : [dir]