An algorithm of discovering signatures from DNA databases on a computer cluster

Abstract

BackgroundSignatures are short sequences that are unique and not similar to any other sequence in a database that can be used as the basis to identify different species. Even though several signature discovery algorithms have been proposed in the past, these algorithms require the entirety of databases to be loaded in the memory, thus restricting the amount of data that they can process. It makes those algorithms unable to process databases with large amounts of data. Also, those algorithms use sequential models and have slower discovery speeds, meaning that the efficiency can be improved.ResultsIn this research, we are debuting the utilization of a divide-and-conquer strategy in signature discovery and have proposed a parallel signature discovery algorithm on a computer cluster. The algorithm applies the divide-and-conquer strategy to solve the problem posed to the existing algorithms where they are unable to process large databases and uses a parallel computing mechanism to effectively improve the efficiency of signature discovery. Even when run with just the memory of regular personal computers, the algorithm can still process large databases such as the human whole-genome EST database which were previously unable to be processed by the existing algorithms.ConclusionsThe algorithm proposed in this research is not limited by the amount of usable memory and can rapidly find signatures in large databases, making it useful in applications such as Next Generation Sequencing and other large database analysis and processing. The implementation of the proposed algorithm is available athttp://www.cs.pu.edu.tw/~fang/DDCSDPrograms/DDCSD.htm.

matK-QR classifier: a patterns based approach for plant species identification

“…Here we present a signatures-based search method and the corresponding software tool, matK -QR Classifier on the Windows platform (http://www.neeri.res.in/matk_classifier/index.htm), which is different from the early tools in the set of predictive nucleotide patterns and the method of sequence classification. Molecular signatures (here we referred as a regular expression) are defined as DNA nucleotide motifs that are unique and present in target species but different from other species sequences [25]. …”

Optimising sampling designs for the maximum coverage problem of plume detection

“…If the detection limit is improved in one of the branches, the worse results of other branches can be ignored when combining them-an idea derived from Lee and Sheu (2014).…”

Evaluating the effect of mutations and ligand binding on transthyretin homotetramer dynamics

“…Normal mode analysis has been calculated using the coarse-grained Elastic Network Model (ENM)[ 23 ],[ 24 ],[ 25 ],[ 26 ],[ 27 ]. Normal modes and molecular dynamics, with the help of powerful computational tools that allow further structural and dynamics analysis[ 28 ],[ 29 ], become standard techniques for analyzing and enhancing our understanding of molecular mechanisms. Briefly, ENM represents the N residues of a protein by their α-carbons (nodes), connected by uniform springs to their neighbours within a cut-off distance r c .…”