The Infona portal uses cookies, i.e. strings of text saved by a browser on the user's device. The portal can access those files and use them to remember the user's data, such as their chosen settings (screen view, interface language, etc.), or their login data. By using the Infona portal the user accepts automatic saving and using this information for portal operation purposes. More information on the subject can be found in the Privacy Policy and Terms of Service. By closing this window the user confirms that they have read the information on cookie usage, and they accept the privacy policy and the way cookies are used by the portal. You can change the cookie settings in your browser.
Constructing genome-wide gene regulatory networks from large-scale gene expression data is an important problem in systems biology. While several techniques have been developed, none of them is parallel, and they do not scale to the whole genome level or incorporate the largest data sets, particularly with rigorous statistical techniques. In this paper, we present a parallel method integrating mutual...
The growing size of sequence, protein and other biological databases results in an increased computational complexity of the analysis process. Often parallelization is the only solution to limit the turnaround time within reasonable limits. Most scalability studies focus on the parallel algorithm and the resulting communication and synchronization patterns of the implementations. In this paper we...
Sequence alignment is a fundamental problem in the computational biology. Many alignment methods have been proposed in the literature, such as pair-wise sequence alignment (2SA), syntenic alignment, multiple sequence alignment (MSA) and constraint multiple sequence alignment, etc. Three-sequence alignment (3SA) problem has been proposed and discussed in the computational biology and proved that the...
Analyzing gene expression patterns is becoming a highly relevant task in the bio informatics area. This analysis makes it possible to determine the behavior patterns of genes under various conditions, a fundamental information for treating diseases, among other applications. An advance in this area is the tricluster algorithm, which is the first algorithm capable of determining 3D clusters, that is,...
The algorithm proposed by Smith-Waterman is an exact method that obtains optimal local alignments in quadratic space and time. For long sequences, quadratic complexity makes the use of this algorithm impractical. In this scenario, parallel computing is a very attractive alternative. In this paper, we propose and evaluate z-align, a parallel exact strategy based on the divergence concept to locally...
This paper presents a heuristic for finding close to optimal solutions to the local alignment problem of two DNA sequences, and more precisely to the gene prediction problem on the Connex Array circuit, a new hierarchical parallel in-memory device. Though not optimal, the solutions generated by our algorithm compare well with those generated by other algorithms in the public domain. When aligning...
A fast algorithm named FAST_LCS is presented for the longest common substring (LCS) problem. The algorithm firstly seeks the successors of the initial identical character tuples according to successor tables to obtain all the identical tuples and their levels. Then the result of LCS can be obtained by tracing back from the identical character tuple with the largest level. For n biosequences X 1, X...
Searching for the longest common subsequence (LCS) of biosequences is one of the most important problems in bioinformatics. A fast algorithm for LCS problem FAST_LCS is presented. The algorithm first seeks the successors of the initial identical character pairs according to a successor table to obtain all the identical pairs and their levels. By tracing back from the identical character pair at the...
RNA secondary structure prediction remains one of the most compelling, yet elusive areas of computational biology. Many computational methods have been proposed in an attempt to predict RNA secondary structures. A popular dynamic programming (DP) algorithm uses a stochastic context-free grammar to model RNA secondary structures, its time complexity is O(N4) and spatial complexity is O(N3 ), where...
Multiple sequence alignment is a fundamental and challenging problem in computational molecular biology. ClustalW, the most widely used multiple sequence alignment software, performs very slowly on hundreds of sequence. Here, we analyze the algorithm complexity of ClustalW as well as the time profile in practice, and then propose a strategy which uses the reconfigurable hardware FPGA to accelerate...
We present faster sequential and parallel algorithms for computing the solvent accessible surface area (ASA) of protein molecules. The ASA can be obtained by calculating the exposed surface area of the spheres obtained by increasing the van der Waals' radii of the atoms with the van der Waals' radius of the solvent. Using domain specific knowledge, we show that the number of sphere intersections is...
Set the date range to filter the displayed results. You can set a starting date, ending date or both. You can enter the dates manually or choose them from the calendar.