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BMCBI
2010
133views more  BMCBI 2010»
13 years 4 months ago
Improving de novo sequence assembly using machine learning and comparative genomics for overlap correction
Background: With the rapid expansion of DNA sequencing databases, it is now feasible to identify relevant information from prior sequencing projects and completed genomes and appl...
Lance E. Palmer, Mathäus Dejori, Randall A. B...
BMCBI
2006
111views more  BMCBI 2006»
13 years 4 months ago
Using ESTs to improve the accuracy of de novo gene prediction
Background: ESTs are a tremendous resource for determining the exon-intron structures of genes, but even extensive EST sequencing tends to leave many exons and genes untouched. Ge...
Chaochun Wei, Michael R. Brent
BMCBI
2011
12 years 11 months ago
DecGPU: distributed error correction on massively parallel graphics processing units using CUDA and MPI
Background: Next-generation sequencing technologies have led to the high-throughput production of sequence data (reads) at low cost. However, these reads are significantly shorter...
Yongchao Liu, Bertil Schmidt, Douglas L. Maskell
BMCBI
2010
154views more  BMCBI 2010»
13 years 4 months ago
An algorithm for automated closure during assembly
Background: Finishing is the process of improving the quality and utility of draft genome sequences generated by shotgun sequencing and computational assembly. Finishing can invol...
Sergey Koren, Jason R. Miller, Brian Walenz, Grang...
BMCBI
2008
101views more  BMCBI 2008»
13 years 4 months ago
Reranking candidate gene models with cross-species comparison for improved gene prediction
Background: Most gene finders score candidate gene models with state-based methods, typically HMMs, by combining local properties (coding potential, splice donor and acceptor patt...
Qian Liu, Koby Crammer, Fernando C. N. Pereira, Da...