Mon, 12/16/2013
Customer is a Duke University professor, and asks about assembling longer contigs for human centromeres. This is a challenging task due to the heavily repeated nature of the centromere sequence.
Mon, 12/16/2013 at 10:48 AM
AccuraScience LB: I am sorry to say that from bioinformatics point of view, de novo assembly of centromeres is currently an unsolved problem. The best attempt in this line of development was made using Sanger sequencing with the haploid portions of the genome only (X and Y chromosomes): http://arxiv.org/abs/1307.0035. Researchers have learned to live with this difficulty, and have tried to investigate centromere sequences without a good assembly, e.g., http://www.ncbi.nlm.nih.gov/pubmed/21081712.
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Note: LB stands for Lead Bioinformatician. An AccuraScience LB is a senior bioinformatics expert and leader of an AccuraScience data analysis team.
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