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
ScalaBLAST 2.0
TL;DR: ScalaBLAST has been designed to run on conventional multiprocessor systems with an eye to extreme parallelism, enabling parallel BLAST calculations using >16 000 processing cores with a portable, robust, fault-resilient design that introduces little to no overhead with respect to serial BLAST.
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A new pheromone trail-based genetic algorithm for comparative genome assembly.
TL;DR: A novel algorithm to align contigs with more than one reference genome at a time is proposed, which can successfully overcome the limitations of low degrees of conserved gene order for the reference and target genomes.
An integrated toolkit for accurate prediction and analysis of cis-regulatory motifs at a genome scale
TL;DR: The comparison results on Escherichia coli K12 genome and the human genome show that BoBro2.0 can identify the statistically significant motifs at a genome scale more efficiently, identify motif instances more accurately and get more reliable motif clusters than MEME.
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e-RGA: enhanced Reference Guided Assembly of Complex Genomes
TL;DR: A novel method is proposed that aims to improve de novo assembly in the presence of a closely related reference in order to obtain enhanced results.
A bioinformatician's guide to the forefront of suffix array construction
Martin C. Frith,Paul Horton +1 more
- 01 Jan 2014
TL;DR: The SA-IS algorithm as mentioned in this paper is the state-of-the-art in suffix array construction, and DisLex is a technique that allows standard suffix array constructions to be modified to enable a simple form of inexact matching needed to support spaced seeds and subset seeds.