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The fragment was cleaved with BanI resulting in a 256 bp long fragment (position −157 to −99, relative to the +1 start site).
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The chromosomal assemblies were sampled at every 130 Kb and at each positions a 6 Kb long fragment was picked (global sampling database).
Step 2. A Lempel-Ziv decomposition of ŋ into m consecutive fragments, ŋ [1: i1] ŋ [ i1+1: i2]... ŋ [ i m -1: L], was computed, such that ŋ [ i k -1+1: i k ] was the longest fragment downstream of position i k-1 for which a direct repeat occurred starting from position j(k) somewhere upstream of position i k -1+1, and ŋ [ i k-1 +1: i k ] did not contain #.
The problem becomes much more complicated when paired end reads are considered since paired-end reads usually span a long fragment, which can be as long as a few hundred positions.
A Lempel-Ziv decomposition of S is a partition of S into m consecutive fragments, S = S [1: i1] S [ i1+1: i2]... S [ i m -1: L], such that the k-th component S [ ik-1+1: i k ] is the longest fragment downstream of position i k -1 for which an exact repeat has been encountered somewhere upstream of position i k -1+1.
When fragments were arbitrarily separated into size classes of <110 bp and >110 bp, we found little difference in the CENP-A-FLAG profiles, indicating that the failure to resolve fixed nucleosome positions is not a result of poor mapping resolution because of long fragment lengths.
Small fragment is easier to amplify than long fragment in PCR reactions.
Run the DNA long enough for the short fragment (520 basepairs) to be separated from the long fragment (3000 basepairs).
The method produces 26 bp long fragments (26 bp tags) from defined positions in cDNAs, providing sufficient sequence information to unambiguously characterize the mRNAs.
The short DNA fragments shift faster than the long fragments, and the shift rate of DNA fragments is promoted by increasing the voltage of electrophoresis.
long fragments (> 1500 nt).
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