BioMed Central Blog

False duplications in genome assemblies

David Kelley and Steven Salzberg at the University of Maryland have developed a pipeline to correct misassembles due to false duplications, in a study published today in Genome Biology. Diploid genomes harbour a significant amount of variation between homologous chromosomes. This causes problems for genome assembly algorithms which may construct two DNA sequences corresponding to one divergent region and incorporate both into an assembly as a false segmental duplication.

Their approach is to align DNA sequence fragments to the surrounding sequence, using mate pair information, to determine whether duplicated segments should be merged into one copy. Mate pairs are two sequence reads derived from the same region of DNA and this study is the first time in which mate pair reads have been used to detect duplications. Kelley and Salzberg apply their pipeline to the cow, chimpanzee, dog and chicken genomes and they identify many single copy regions that have been falsely incorporated as segmental duplications in these genome assemblies, which also allows previously undetected polymorphisms to be identified.  This promises to be a valuable method for correcting existing errors in many genome assemblies and to control for misassembly errors in future genome sequencing efforts.

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Highlights from the latest issue of Arthritis Research & Therapy

In each print edition of Arthritis Research & Therapy the Editors-in-Chief, Profs Ravinder Maini and Peter Lipsky, highlight articles that are of special interest to the journal's readership – the Editors’ choice.

In the latest issue, a feasibility trial by Ng and colleagues found that a combination of glucosamine sulphate supplementation and walking for approximately 30 minutes a day, three times a week, significantly reduced pain and improved physical function in osteoarthritis patients.

Another selection by the Editors is a study by Schurgers et al which highlights the discrepancy between the in vitro and in vivo effects of mesenchymal stem cells.  The team of researchers from Katholieke Universiteit Leuven, Belgium, demonstrated that murine bone marrow-derived mesenchymal stem cells dose-dependently suppress T cell proliferation in vitro, but are unable to influence the disease course in a mouse model of collagen-induced arthritis.

Also making the Editors' choice is a comprehensive review article examining the contribution of genetic variation and infection to the pathogenesis of anti-neutrophil cytoplasmic antibody-associated systemic vasculitis, with a focus on the role of autoantibodies to the membrance protein LAMP-2.

All research published in Arthritis Research & Therapy is open access; reviews published within the previous 6 months require a subscription. Visit the journal website to view the latest articles published in the journal.

Abigail Jones

Senior Assistant Editor - Arthritis Research & Therapy

Posted by Frances Mulvany at 09:41    Comments (0)