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Exact(4)
The detailed device parameters in the simulations are as follows: the thickness of bulk silicon (T si) is 20 nm; the lengths of Gate1 (Lg1) and Gate2 (Lg2) are 400 nm and 200 nm, respectively; the length of gap (L gap) between Gate1 and Gate2 is 50 nm; the thickness of gate oxide (HfO2) (T oxide) is 3 nm.
The maximal length of gap size between palindromic repeats was restricted to 3 kb.
This is presumably a consequence of a decline in the length of gap relative to the length of contig and scaffolds as more scaffolds are joined.
The affine gap penalty, i.e., the penalty increasing linearly with the length of gap after the initial gap opening penalty, was used for gap opening (-4) and gap extension (-2).
Similar(56)
Length of gaps were controlled and contigs joined through large stretches (>10Kb) of Ns were separated.
To assess the quality of the data set, we evaluated the assembled unigenes to determine the presence and length of gaps in the sequences.
In the latter case alignment information (position and length of gaps) can be imported back into the annotated dataset in ProSeq3.
Many real motifs contain positions of low information (gaps), but the existing algorithms usually do not allow gaps, or require a user to specify the exact location and length of gaps, which is often impractical for real applications.
There were more gaps with lengths greater than 3424 bp than expected using the global mean gap length of 584 bp and more gaps with lengths greater than 468 bp than expected using the mean length of gaps < 1000 bp (data not shown).
Additionally, we restricted the length of gaps in the colinear chaining algorithm to 2000 bp on the E.coli and P.syringae datasets and to 5000 bp on the C.elegans and human datasets.
Because even small genomic variations may occasionally change the functions of genes, we filtered the original 5097 LCBs using a strict cutoff value (1.01), which means the length of gaps in each LCB is smaller than 1% of the length of the non-gap regions.
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