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Here, it resulted in a total of 885 iterations taking 5 h 6 min on an Intel(R) Xeon(TM) CPU 3.40 GHz CPU, less than the 5 h 36 min needed for the segmentation algorithm of Huber et al. (2006) with maximum segment length l = 1000 (22 000 bp) and segment number on each strand S = 1500.
We require the difference between the maximum segment length and the minimum segment length to be less than 25% of the mean segment length over a moving time period of 60 seconds.
We used the maximum segment length (NFFT in Matlab) possible, (i.e. spectral resolution at the expense of accuracy) using 1,200 and 180 samples for the post-transient and transient periods, respectively.
For the comparison of the new HMM segmentation method and the piecewise constant regression implemented in the algorithm of Huber et al. (2006), the later was run on the data after correction for difference of affinity between probes (as shown in Fig. 3) with maximum segment length l = 22000 bp and number of segments on each strand S between 1000 and 3000.
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This was created by manually digitising all drains within each reference area resulting in reference dataset extending to 76,635 m (minimum and maximum segment lengths of 0.35 435 m).
Also, a minimum number of line votes of 20 and a value of 5 for the minimum segment length and the maximum gap of points of the same line have been used.
Passed filter reads were mapped onto the sorghum reference genome by using Bowtie (0.12.7) [ 23], and TopHat (1.1.4) [ 24] with the following options: segment length, 25; minimum intron length, 30; maximum intron length, 6000; maximum multihits, 40; number of threads: 2. Cufflinks (0.9.3) [ 25] was used for prediction of genes by the piling-up of mapped reads.
The M-mode values of left ventricular dimensions were confirmed by measurements of multiple left ventricular wall segments from several 2-D views and cats were classified to have fHCM if the maximum diastolic wall thickness in any segment exceeded 5.5 mm in > 50% of segment length.
In all simulations, the length of the queue at routers is set to 50 kbytes and the maximum segment size of TCP is 512 bytes.
Parameters for Tophat were as follows: segment length = 40; initial read mismatch = 2; splice mismatch = 0; segment mismatch = 2; maximum insertion length = 1; and maximum deletion length = 1.
Evaluation for Segment Length.
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