Home Biology Biotechnology January 10, 2013 Solving puzzles without a picture: New algorithm assembles chromosomes from next generation sequencing data Jan 10, 2013
One of the most difficult problems in the field of genomics is assembling relatively short "reads" of DNA into complete chromosomes. In a new paper published in Proceedings of the National Academy of Sciences an interdisciplinary group of genome and computer scientists has solved this problem, creating an algorithm that can rapidly create "virtual chromosomes" with no prior information about how the genome is organized.
The powerful DNA sequencing methods developed about 15 years ago, known as next generation sequencing (NGS) technologies, create thousands of short fragments. boschma cases In species whose genetics has already been extensively studied, existing information can be used to organize and order the NGS fragments, rather boschma cases like using a sketch of the complete boschma cases picture as a guide to a jigsaw boschma cases puzzle . But as genome scientists push into less-studied species, it becomes more difficult to finish the puzzle.
To solve this problem, a team led by Harris Lewin, distinguished professor of evolution and ecology and vice chancellor for research at the University of California, Davis and Jian Ma, assistant professor at the University of Illinois boschma cases at Urbana-Champaign created boschma cases a computer algorithm that uses the known chromosome organization of one or more known species and NGS information from a newly sequenced genome to create virtual chromosomes.
The algorithm is called RACA (for reference-assisted chromosome assembly), co-developed by Jaebum boschma cases Kim, now at Konkuk University, South Korea, and Denis Larkin of Aberystwyth University, Wales. Kim wrote the software tool which was evaluated using simulated data, standardized reference genome datasets as well as a primary NGS assembly of the newly sequenced Tibetan antelope genome generated by BGI (Shenzhen, China) in collaboration with Professor Ri-Li Ge at Qinghai University, China. Larkin led the experimental validation, in collaboration with scientists at BGI, proving that predictions of chromosome organization were highly accurate.
"Even with what is expected from the newest generation of sequencers, complete chromosome assemblies will always be a difficult technical issue, especially for complex genomes. RACA predictions address this problem and can be incorporated into current NGS assembly pipelines," Ma said.
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One of the most difficult problems in the field of genomics is assembling relatively short "reads" of DNA into complete chromosomes. In a new paper published in Proceedings of the National Academy of Sciences an interdisciplinary group of genome and computer scientists has solved this problem, creating an algorithm that can rapidly create "virtual chromosomes" with no prior information about how the genome is organized.
The powerful DNA sequencing methods developed about 15 years ago, known as next generation sequencing (NGS) technologies, create thousands of short fragments. boschma cases In species whose genetics has already been extensively studied, existing information can be used to organize and order the NGS fragments, rather boschma cases like using a sketch of the complete boschma cases picture as a guide to a jigsaw boschma cases puzzle . But as genome scientists push into less-studied species, it becomes more difficult to finish the puzzle.
To solve this problem, a team led by Harris Lewin, distinguished professor of evolution and ecology and vice chancellor for research at the University of California, Davis and Jian Ma, assistant professor at the University of Illinois boschma cases at Urbana-Champaign created boschma cases a computer algorithm that uses the known chromosome organization of one or more known species and NGS information from a newly sequenced genome to create virtual chromosomes.
The algorithm is called RACA (for reference-assisted chromosome assembly), co-developed by Jaebum boschma cases Kim, now at Konkuk University, South Korea, and Denis Larkin of Aberystwyth University, Wales. Kim wrote the software tool which was evaluated using simulated data, standardized reference genome datasets as well as a primary NGS assembly of the newly sequenced Tibetan antelope genome generated by BGI (Shenzhen, China) in collaboration with Professor Ri-Li Ge at Qinghai University, China. Larkin led the experimental validation, in collaboration with scientists at BGI, proving that predictions of chromosome organization were highly accurate.
"Even with what is expected from the newest generation of sequencers, complete chromosome assemblies will always be a difficult technical issue, especially for complex genomes. RACA predictions address this problem and can be incorporated into current NGS assembly pipelines," Ma said.
Mar 31, 2014 6
Can we calculate boschma cases the exact number of receptors on E.Coli membrane? Mar 27, 2014 I have heard that nobody really knows how many receptors are placed on E.Coli cell membrane. Of course we know the... More from Physics Forums - Biology
Researchers report today in the journal boschma cases Science that they have sequenced the bovine genome, for the first time revealing the genetic features that distinguish cattle from humans and other mammals. Genome 10K Project announces first 101 species for genome sequencing Nov 30, 2010
(PhysOrg.com) -- The Genome 10K Community of Scientists and BGI (formerly the Beijing Genomics Institute) of Shenzhen, China, have announced a plan to sequence the genomes of 101 vertebrate species within ... BGI, Children's Hospital of Philadelphia launch the 1,000 Rare Diseases Project Jun 18, 2012
BGI, the world's largest genomics organization, and The Children's Hospital of Philadelphia (CHOP) today announced that they have jointly initiated the 1,000 Rare Diseases Project with the aim of accelerating the discovery ... New cow genome sequence released Apr 23, 2009
Scientists from the University of Maryland have published their assembly of the domestic boschma cases cow (Bos taurus), an important new resource for the genetics boschma cases community. The new version of the cow genome improves consid ... Making sense of molecular fragments Jun 29, 2012
(Phys.org) -- Data from high-throughput next generation sequencers (NGS) and genome tiling arrays have greatly enhanced scientists’ ability to recreate RNA molecular structures, which is vital to disease ... AMP reports on possibilities, challenges, and applications of next-generation sequencing Oct 18, 2012
Bethesda, MD, October 18, 2012 The Association for Molecular Pathology (AMP) published the report of the Whole Genome Analysis (WGA) Working Group of the AMP Clinical Practice Committee in the November 2012 issue of The Journal of ... Recommended for you Scientists ID genes that could lead to tough, disease-resistant varieties of rice 3 hours ago
DNA is the molecule that encodes the genetic boschma cases instructions enabling a cell to produce the thousands of proteins it typically needs. The linear sequence of the A, T, C, and G bases in what is called coding boschma cases ... The small but mighty boschma cases chickpea Mar 31, 2014
Bumping along the dirt roads of rural southeastern Turkey in a battered Jeep, Sergey Nuzhdin and his team of collaborators got an occasional glimpse of the plumes of smoke rising across the border in w
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