Assembling a genome from fragments of DNA sequence is often compared to assembling a puzzle. One of the problems researchers face with the increasing use of next-generation sequencing technologies is that the pieces of DNA sequence generated by the 454 or Illumina platforms are much smaller and far more numerous than those produced by the Sanger platform. Assembling these pieces into a genome for study is both costly and time-consuming.
DOE JGI researchers led by Deputy Director of Genomic Technologies Len Pennacchio and Advanced Sequencing Group head Feng Chen have developed a way to more efficiently assemble the short DNA segments.
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DOE JGI researchers developed CLIP-PE for the de novo assembly of short reads.
(Image by MyklRoventine, Fotopedia/CC2.0)
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As detailed in an article published January 9, 2012 in PLoS ONE, their approach involves the use of mate pairs, two short segments of DNA separated by an insert that can help align and orient the sequences across perceived gaps in a genome during the assembly process.
Chen and his colleagues developed a novel Cre-LoxP Inverse PCR Paired-End (CLIP-PE) methodology of quickly generating mate-pair libraries, which allow for a wide variety of possible combinations of the short sequences so that researchers can assemble a genome with fewer gaps, which in turn helps reduce the finishing costs. The team tested the method by generating Illumina mate pair libraries of 5 kb, 12 kb and 22 kb.