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
Whole genome assembly of a natto production strain Bacillus subtilis natto from very short read data
Yukari Nishito,Yasunori Osana,Tsuyoshi Hachiya,Kris Popendorf,Atsushi Toyoda,Asao Fujiyama,Mitsuhiro Itaya,Yasubumi Sakakibara +7 more
TL;DR: The determination of the whole genome sequence of Bacillus subtilis natto provided detailed analyses of a set of genes related to natto production, demonstrating the number and locations of insertion sequences that B. subtil is natto harbors but B.subilis 168 lacks.
De novo assembly of the Pseudomonas syringae pv. syringae B728a genome using Illumina/Solexa short sequence reads.
TL;DR: It is demonstrated that, in practice, de novo assembly of 36-nucleotide reads can generate reasonably accurate assemblies from about 40 x deep sequence data sets, which are useful for exploring an organism's proteomic potential, at a very economic low cost.
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G-BLASTN: accelerating nucleotide alignment by graphics processors
Kaiyong Zhao,Xiaowen Chu +1 more
TL;DR: G-BLastN is a GPU-accelerated nucleotide alignment tool based on the widely used NCBI-BLAST that can produce exactly the same results as NCBI -BLAST, and it has very similar user commands.
Whole genome sequencing of the black grouse ( Tetrao tetrix ): reference guided assembly suggests faster-Z and MHC evolution
TL;DR: The results support the hypothesis that the chromosome X (Z) evolves faster than the autosomes and the data are consistent with the MHC regions being more liable to change than the genome average.
A bioinformatician’s guide to the forefront of suffix array construction algorithms
TL;DR: DisLex, a technique that allows standard suffix array construction algorithms to create modified suffix arrays designed to enable a simple form of inexact matching needed to support ‘spaced seeds’ and ‘subset seeds” used in many biological applications is described.
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