Seqdev: an algorithm for constructing genetic elements using comparative assembly
Tasnim Rahman,Hasnain Heickal,Shamira Tabrejee,Miraj Kobad Chowdhury,Sheikh Muhammad Sarwar,Mohammad Shoyaib +5 more
TL;DR: This article was published in Plant Tissue Culture and Biotechnology [© 2016, Bangladesh Association for plant Tissue] and the definite version is available at: http://dx.doi.org/10.3329/ptcb.v26i1.29772.
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Abstract: This article was published in Plant Tissue Culture and Biotechnology [© 2016, Bangladesh Association for Plant Tissue] and the definite version is available at: http://dx.doi.org/10.3329/ptcb.v26i1.29772. The Journal's website is at: http://www.banglajol.info/index.php/PTCB/article/view/29772
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References
Gene-Boosted Assembly of a Novel Bacterial Genome from Very Short Reads
TL;DR: This study demonstrates the feasibility of very short read sequencing for the sequencing of bacterial genomes, particularly those for which a related species has been sequenced previously, and expands the potential application of this new technology to most known prokaryotic species.
HiTEC: accurate error correction in high-throughput sequencing data
TL;DR: HiTEC is presented, an algorithm that provides a highly accurate, robust and fully automated method to correct reads produced by high-throughput sequencing methods and provides significantly higher accuracy than previous methods.
BFAST: an alignment tool for large scale genome resequencing.
TL;DR: It is shown BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods.
Computability of models for sequence assembly
Paul Medvedev,Konstantinos Georgiou,Gene Myers,Michael Brudno +3 more
- 08 Sep 2007
TL;DR: This work shows sequence assembly to be NP-hard under two different models: string graphs and de Bruijn graphs, and gives the first, to the knowledge, optimal polynomial time algorithm for genome assembly that explicitly models the double-strandedness of DNA.
Root-specific transcript profiling of contrasting rice genotypes in response to salinity stress.
Olivier Cotsaftis,Darren Plett,Alexander W. Johnson,Alexander W. Johnson,Harkamal Walia,Harkamal Walia,Clyde Wilson,Abdelbagi M. Ismail,Timothy J. Close,Mark Tester,Ute Baumann +10 more
TL;DR: In this article, the authors compared transcript levels in rice (Oryza sativa) shoots of FL478, a salt-tolerant indica recombinant inbred line, and IR29, a sal-sensitive cultivar, to identify genes likely to be involved in plant salinity tolerance rather than in responses to salinity per se.