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To evaluate the medium insert size, 86 randomly chosen BACs were digested with NotI enzyme and analysed by pulsed field gel electrophoresis.
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Libraries HVVMRXALLhA and HVVMRXALLhB contributed clones with medium insert sizes between 97 Kb and 100 Kb.
Therefore, medium inserts sizes were applied for these two clones in our estimation of genome coverage.
To close the gaps and to raise the quality of the sequences, primer walking on the medium and small insert size clones, and PCR/adapter PCR [42] on the MDA products were performed.
Here, we modified existing MP library construction protocols to allow for the generation of a wide range of small, medium and large insert size mate-pair libraries (3 kb up to 25 kb) and present a systematic comparison of their individual and combined utility for exploring mammalian genome structure.
The draft phase involved two clone libraries, one small insert library (2200 bp average insert size) and one medium insert library (6289 bp average insert size).
Conversely, input level did not have an effect on insert size distributions (high, medium and low) (ANOVA, p > 0.05) (Additional file 1: Table S3).
The DNA was fragmented by kinetic shearing, and three shotgun libraries were generated: small and medium insert libraries in the plasmid pOTWI3 (using size fractions of 2-3 kb and 6-8 kb, respectively), and a large insert fosmid library in pEpiFOS-5 (insert sizes ranging from 28-47 kb), which was used as a scaffold.
Different techniques are used to detect insertions that are short (shorter than the reads), medium (of size between read length and insert size) or long (of size exceeding insert size).
Figure 2 Distribution of insert size.
Figure 1 Detection of insert size.
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