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The Viterbi algorithm is the compute-intensive kernel in Hidden Markov Model (HMM) based sequence alignment applications. In this paper, we investigate extending several parallel methods, such as the wave-front and streaming methods for the Smith-Waterman algorithm, to achieve a significant speed-up on a GPU. The wave-front method can take advantage of the computing power of the GPU but it cannot...
We designed a new genome search tool, basic sequence search by hashing algorithm (BSSHA) bases on basic local alignment search tool (BLAST) and, sequence search and alignment by hashing algorithm (SSAHA) for DNA sequence databases. Preprocess query sequence by making m-letter word list. Sequences in the database are preprocessed by breaking them into k-tuples of k-contiguous bases and hash table is...
With the remarkable increase in the number of nucleotide and acid sequences, it is necessary to study pattern matching in querying sequence patterns in the biological sequence database. To further raise the performance of the pattern matching algorithm, an improved BM algorithm (called BMBR) is presented. It bases on the method of BM algorithm and combines with the shift function of BR algorithm,...
For computer scientists the problem of biological data retrieval has become synonymous with homology-based retrieval of primary gene sequence data and their associated protein products. This perspective is accessible to computer scientists, as primary sequence data is modeled as strings and fundamental algorithmic tools can be applied. However, by sticking with this formative foundation, we computer...
Similarity search in sequence databases is of paramount importance in bioinformatics research. As the size of the genomic databases increases, similarity search of proteins in these databases becomes a bottle-neck in large-scale studies, calling for more efficient methods of content-based retrieval. In this study, we present a metric-preserving, landmark-guided embedding approach to represent sequences...
In this study, the effects of the scoring functions, which are used in multiple sequence alignment problem, to find the biologically meaningful alignment has been investigated. BALiBASE version 3 has been used as benchmark set. Results have been obtained by calculating score values for alignments in benchmark set and investigating whether the higher score is possible for benchmark alignment or not.
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...
Sequence alignment is a common and often repeated task in molecular biology. Typical alignment operations consist of finding similarities between a pair of sequences (pairwise sequence alignment) or a family of sequences (multiple sequence alignment). The need for speeding up this treatment comes from the rapid growth rate of biological sequence databases: every year their size increases by a factor...
Protein sequence clustering has been widely used as a part of the analysis of protein structure and function. In most cases single link or graph-based clustering algorithms have been applied. In this paper, we demonstrate an approach of clustering proteins, SEQOPTICS (sequence clustering with OPTICS), which is based on OPTICS (ordering points to identify the clustering structure), an attractive approach...
The underlying assumption of many automated sequence annotation methods is that similar sequences imply similar biological functions. The present paper re-examines this assumption. A novel measure based on a set of local BLAST alignments is introduced to define the overall similarity between two protein sequences. The relationships between yeast protein sequences and their biological functions in...
The problem of finding the shortest common supersequence (SCS) of a set of sequences is an important problem with applications in many areas. It is also a key problem in biological sequences analysis. However, the problem is well-known to be NP-complete. Many heuristic algorithms have been proposed. However, the performances of many current heuristic algorithms are not very good, especially on many...
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