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
BLASTAssemb: An approach to construct genetic elements using BLAST
Tasnim Rahman,Tasnova Chowdhury,Shamira Tabrejee,Md. Miraj Kobad Chowdhury,Mohammad Shoyaib +4 more
- 01 Dec 2014
TL;DR: Experimental results demonstrated that the proposed algorithm could accurately construct the promoter sequences of Pokkali from its raw genome sequences and the capability of BLAST, which enables the construction of genetic elements from raw sequences.
1
ALLPATHS: de novo assembly of whole-genome shotgun microreads.
Jonathan Butler,Iain MacCallum,Michael Kleber,Ilya Shlyakhter,Matthew K. Belmonte,Eric S. Lander,Chad Nusbaum,David B. Jaffe +7 more
TL;DR: A general method for genome assembly that can be applied to all types of DNA sequence data, not only short read data, but also conventional sequence reads is described.
Comparative genome assembly
TL;DR: A novel algorithm for comparative genome assembly that can accurately assemble a typical bacterial genome in less than four minutes on a standard desktop computer is described.
Bioinformatics challenges of new sequencing technology
Mihai Pop,Steven L. Salzberg +1 more
TL;DR: Challenges arising from using new DNA sequencing technologies in assembly projects, both de novo and for resequencing purposes, as well as efforts to improve genome annotation in the fragmented assemblies produced by short read lengths are addressed.
Reference-guided assembly of four diverse Arabidopsis thaliana genomes
Korbinian Schneeberger,Stephan Ossowski,Felix Ott,Juliane D. Klein,Xi Wang,Christa Lanz,Lisa M. Smith,Jun Cao,Joffrey Fitz,Norman Warthmann,Stefan R. Henz,Daniel H. Huson,Detlef Weigel +12 more
TL;DR: Reference-guided whole-genome assemblies of four divergent Arabidopsis thaliana strains that complement the 125-Mb reference genome sequence released a decade ago were presented in this paper.