Pairwise Sequence Alignment Algorithm Research Articles

Correctness by Construction for Pairwise Sequence Alignment Algorithm in Bio-Sequence

Correctness by Construction for Pairwise Sequence Alignment Algorithm in Bio-Sequence

A biological sub-sequences detection using integrated BA-PSO based on infection propagation mechanism: Case study COVID-19

The longest common consecutive subsequences (LCCS) play a vital role in revealing the biological relationships between DNA/RNA sequences especially the newly discovered ones such as COVID-19. FLAT is a Fragmented local aligner technique which is an accelerated version of the local pairwise sequence alignment algorithm based on meta-heuristic algorithms. The performance of FLAT needs to be enhanced since the huge length of biological sequences leads to trapping in local optima. This paper introduces a modified version of FLAT based on improving the performance of the BA algorithm by integration with particle swarm optimization (PSO) algorithm based on a novel infection mechanism. The proposed algorithm, named BPINF, depends on finding the best-explored solution using BA operators which can infect the agents during the exploitation phase using PSO operators to move toward it instead of moving toward the best-exploited solution. Hence, moving the solutions toward the two best solutions increase the diversity of generated solutions and avoids trapping in local optima. The infection can be propagated through the agents where each infected agent can transfer the infection to other non-infected agents which enhances the diversification of generated solutions. FLAT using the proposed technique (BPINF) was validated to detect LCCS between a set of real biological sequences with huge lengths besides COVID-19 and other well-known viruses. The performance of BPINF was compared to the enhanced versions of BA in the literature and the relevant studies of FLAT. It has a preponderance to find the LCCS with the highest percentage (88%) which is better than other state-of-the-art methods.

Efficient Multiple Sequences Alignment Algorithm Generation via Components Assembly Under PAR Framework.

As a key algorithm in bioinformatics, sequence alignment algorithm is widely used in sequence similarity analysis and genome sequence database search. Existing research focuses mainly on the specific steps of the algorithm or is for specific problems, lack of high-level abstract domain algorithm framework. Multiple sequence alignment algorithms are more complex, redundant, and difficult to understand, and it is not easy for users to select the appropriate algorithm; some computing errors may occur. Based on our constructed pairwise sequence alignment algorithm component library and the convenient software platform PAR, a few expansion domain components are developed for multiple sequence alignment application domain, and specific multiple sequence alignment algorithm can be designed, and its corresponding program, i.e., C++/Java/Python program, can be generated efficiently and thus enables the improvement of the development efficiency of complex algorithms, as well as accuracy of sequence alignment calculation. A star alignment algorithm is designed and generated to demonstrate the development process.

Pairwise Heuristic Sequence Alignment Algorithm Based on Deep Reinforcement Learning.

Goal: Various methods have been developed to analyze the association between organisms and their genomic sequences. Among them, sequence alignment is the most frequently used method for comparative analysis of biological genomes. We intend to propose a novel pairwise sequence alignment method using deep reinforcement learning to break out the old pairwise alignment algorithms. Methods: We defined the environment and agent to enable reinforcement learning in the sequence alignment system. This novel method, named DQNalign, can immediately determine the next direction by observing the subsequences within the moving window. Results: DQNalign shows superiority in the dissimilar sequence pairs that have low identity values. And theoretically, we confirm that DQNalign has a low dimension for the sequence length in view of the complexity. Conclusions: This research shows the application method of deep reinforcement learning to the sequence alignment system and how deep reinforcement learning can improve the conventional sequence alignment method.

Low power DNA protein sequence alignment using FSM state transition controller

In this paper we proposed an efficient computation technique for DNA patterns on reconfigurable hardware (FPGAs) platform. The paper also presents the results of a comparative study between existing dynamic and heuristic programming methods of the widely-used Smith-Waterman pair-wise sequence alignment algorithm with FSM-based core implementation. Traditional software implication-based sequence alignment methods can not meet the actual data rate requirements. Hardware-based approach will give high scalability and one can process parallel tasks with a large number of new databases. This paper explains finite state machine (FSM)-based core processing element to classify the protein sequence. In addition, we analyse the performance of bit-based sequence alignment algorithms and present the inner stage pipelined field programmable gate array (FPGA) architecture for sequence alignment implementations. Here, synchronised controllers are used to carry out parallel sequence alignment. The complete architecture is designed to carry out parallel processing in hardware, with FSM-based bit wised pattern comparison with scalability as well as with a minimum number of computations. Finally, the proposed design proved to be high performance and its efficiency in terms of resource utilisation is proved on FPGA implementation.

Design and Implementation of Pairwise Sequence Alignment Algorithm Components Based on Dynamic Programming

Design and Implementation of Pairwise Sequence Alignment Algorithm Components Based on Dynamic Programming

MPSAGA: a matrix-based pair-wise sequence alignment algorithm for global alignment with position based sequence representation

The proposed algorithm is a novel matrix-based global pair-wise sequence alignment with a de novo sequence representation. Needleman–Wunsch, noblest, Emboss-Needle, ALIGN, LALIGN, FOGSAA, DIALIGN, ACANA, MUMmer, etc. are few other algorithms that are most commonly used for global pair-wise sequence alignment. Needleman–Wunsch algorithm is one of the most popular algorithms that provides the best possible pair-wise sequence alignment, but the algorithm output is associated with high time and space complexities. To resolve these complex issues, researchers have proposed several algorithms to reduce time and space complexities in the pair-wise sequence alignment. Most of these algorithms provide solutions, but compromise the optimal result in favor of plummeting time and space complexities. An attempt has been made in the present research to develop MPSAGA and a completely unique positional matrix (PM) based sequence representation to deal with the time and space complexities without compromising sequence alignment results (MPSAGA is in public domain available at https://github.com/JyotiLakhani1/MPSAGA ). A benchmarking of the proposed algorithm has also been performed with other popular pair-wise sequence alignment algorithms with and without positional matrix-based sequence representation. The use of an integer instead of string data type and exclusive clustering method in MPSAGA with positional matrix based sequence representation resulted in a noteworthy reduction in the memory usage (space) and execution time in the pair-wise alignment of biological sequences.

A Space-Efficient Approach towards Distantly Homologous Protein Similarity Searches

Protein similarity searches are a routine job for molecular biologists where a query sequence of amino acids needs to be compared and ranked against an ever-growing database of proteins. All available algorithms in this field can be grouped into two categories – either solving the problem using sequence alignment through dynamic programming, or, employing certain heuristic measures to perform an initial screening followed by applying an optimal sequence alignment algorithm to the closest matching candidates. While the first approach suffers from huge time and space demands, the latter approach might miss some protein sequences which are distantly related to the query sequence. In this paper, we propose a heuristic pair-wise sequence alignment algorithm that can be efficiently employed for protein database searches for moderately sized databases. The proposed algorithm is sufficiently fast to be applicable to database searches for short query sequences, has constant auxiliary space requirements, produces good alignments, and is sensitive enough to return even distantly related protein chains that might be of interest. Keywords: sequence alignment, protein similarity search, heuristic algorithm, protein database, bioinformatics

Global and local sequence alignment with a bounded number of gaps

Pairwise sequence alignment techniques have gained renewed interest in recent years, primarily due to their applications in re-sequencing—the assembly of a genome directed by a reference sequence.In this article, we show that adding the flexibility of bounding the number of gaps inserted in an alignment strengthens the classical sequence alignment scheme of scoring matrices and affine gap penalty scores. We present GapsMis, an algorithm for pairwise global sequence alignment with a variable, but bounded, number of gaps. It is based on computing a variant of the traditional dynamic programming matrix for global sequence alignment. We also present GapsMis-L, the analogous algorithm for pairwise local sequence alignment with a variable, but bounded, number of gaps.To test the accuracy of GapsMis and GapsMis-L we performed millions of pairwise sequence alignments under realistic conditions, based on the properties of real full-length genomes. The results show that GapsMis and GapsMis-L can increase the accuracy of extending short-read alignments compared to the traditional approaches. The importance of our contribution is underlined by the fact that the provided algorithms may be seamlessly integrated into any biological pipeline. The open-source code of our implementation is freely available at http://www.inf.kcl.ac.uk/research/projects/gapmis/.

GSWABE: faster GPU‐accelerated sequence alignment with optimal alignment retrieval for short DNA sequences

SummaryIn this paper, we present GSWABE, a graphics processing unit (GPU)‐accelerated pairwise sequence alignment algorithm for a collection of short DNA sequences. This algorithm supports all‐to‐all pairwise global, semi‐global and local alignment, and retrieves optimal alignments on Compute Unified Device Architecture (CUDA)‐enabled GPUs. All of the three alignment types are based on dynamic programming and share almost the same computational pattern. Thus, we have investigated a general tile‐based approach to facilitating fast alignment by deeply exploring the powerful compute capability of CUDA‐enabled GPUs. The performance of GSWABE has been evaluated on a Kepler‐based Tesla K40 GPU using a variety of short DNA sequence datasets. The results show that our algorithm can yield a performance of up to 59.1 billions cell updates per second (GCUPS), 58.5 GCUPS and 50.3 GCUPS for global, semi‐global and local alignment, respectively. Furthermore, on the same system GSWABE runs up to 156.0 times faster than the Streaming SIMD Extensions (SSE)‐based SSW library and up to 102.4 times faster than the CUDA‐based MSA‐CUDA (the first stage) in terms of local alignment. Compared with the CUDA‐based gpu‐pairAlign, GSWABE demonstrates stable and consistent speedups with a maximum speedup of 11.2, 10.7, and 10.6 for global, semi‐global, and local alignment, respectively. Copyright © 2014 John Wiley & Sons, Ltd.

Coarse Grain Load Balance Algorithm for Detecting Similar Regions in DNA and Proteins Sequences

The tremendous quantity and quality of data obtained by conformations of DNA and protein sequences makes their analysis very time consuming, complex, expensive and impractical. Therefore, the feasible way to identify new sequences is to compare them with well-known sequences available in established genetic databank. Comparing sequences may reveal functional, structural, and evolutionary analogies between sequences. Needleman and Wunsch (NW), and Smith and Waterman (SW) algorithms are pioneers in dynamic programming matrix for comparing two sequences with gap penalty function. However, for long sequences both methods contribute toward time and space complexity. FASTA and BLAST are heuristic method based on hitting techniques for fast detection of similar region; unfortunately they produced results with no sensitivity. There remains a need for an efficient method(s) that can detect similar regions in two sequences with accurate results and reasonable time. In this paper, we extend an existing approach to develop an efficient parallel algorithm for pairwise local sequence alignment. Our method is based on load-balancing algorithm with the CPU scheduling technique in order to accelerate the calculation of data-dependency problem in sequences alignment. Using X86-based PC with eight logical processors we able to apply 4 MBP on the proposed algorithm with a speedup of 33% increase compared to the original SW algorithm.

Pairwise sequence alignment for very long sequences on GPUs.

We develop novel single-GPU parallelisations of the Smith-Waterman algorithm for pairwise sequence alignment. Our algorithms, which are suitable for the alignment of a single pair of very long sequences, can be used to determine the alignment score as well as the actual alignment. Experimental results demonstrate an order of magnitude reduction in run time relative to competing GPU algorithms.

Efficient architecture and scheduling technique for pairwise sequence alignment

A novel efficient hardware architecture to optimize the execution time of dynamic programming-based (DP) pairwise sequence alignment algorithms in hardware is proposed. It is realized by introducing an efficient overlapped scheduling of alignment matrix computation and substitution coefficients' pre-loading onto processing elements (PEs) in folded systolic arrays. A new metric is also proposed as an independent performance evaluator to compare different core implementations on different FPGA platforms fairly. Implementation results show that the new hardware architecture for sequence alignment achieves a minimum of 40 percent area normalized speed-up compared to the state-of-the-art hardware implementation, with the speed-up growing linearly with the number of folds e.g. 120 percent speed-up for 16-fold. Compared to equivalent software implementations, the novel hardware architecture achieves a minimum of 103x speed-up, with the speed-up growing linearly with the number of folds e.g. 140x speed-up for 20-fold.

Workflow mining and outlier detection from clinical activity logs

PurposeThe purpose of this study is twofold: (1) to derive a workflow consensus from multiple clinical activity logs and (2) to detect workflow outliers automatically and without prior knowledge from experts. MethodsWorkflow mining is used in this paper to derive consensus workflow from multiple surgical activity logs using tree-guided multiple sequence alignment. To detect outliers, a global pair-wise sequence alignment (Needleman–Wunsch) algorithm is used. The proposed method is validated for Laparoscopic Cholecystectomy (LAPCHOL). ResultsAn activity log is directly derived for each LAPCHOL surgery from laparoscopic video using an already developed instrument tracking tool. We showed that a generic consensus can be derived from surgical activity logs using multi-alignment. In total 26 surgery logs are used to derive the consensus for laparoscopic cholecystectomy. The derived consensus conforms to the main steps of laparoscopic cholecystectomy as described in best practices. Using global pair-wise alignment, we showed that outliers can be detected from surgeries using the consensus and the surgical activity log. ConclusionAlignment techniques can be used to derive consensus and to detect outliers from clinical activity logs. Detecting outliers particularly in surgery is a main step to automatically mine and analyse the underlying cause of these outliers and improve surgical practices.

High Performance Biological Pairwise Sequence Alignment: FPGA versus GPU versus Cell BE versus GPP

This paper explores the pros and cons of reconfigurable computing in the form of FPGAs for high performance efficient computing. In particular, the paper presents the results of a comparative study between three different acceleration technologies, namely, Field Programmable Gate Arrays (FPGAs), Graphics Processor Units (GPUs), and IBM’s Cell Broadband Engine (Cell BE), in the design and implementation of the widely-used Smith-Waterman pairwise sequence alignment algorithm, with general purpose processors as a base reference implementation. Comparison criteria include speed, energy consumption, and purchase and development costs. The study shows that FPGAs largely outperform all other implementation platforms on performance per watt criterion and perform better than all other platforms on performance per dollar criterion, although by a much smaller margin. Cell BE and GPU come second and third, respectively, on both performance per watt and performance per dollar criteria. In general, in order to outperform other technologies on performance per dollar criterion (using currently available hardware and development tools), FPGAs need to achieve at least two orders of magnitude speed-up compared to general-purpose processors and one order of magnitude speed-up compared to domain-specific technologies such as GPUs.

Parallelizing and optimizing a bioinformatics pairwise sequence alignment algorithm for many-core architecture

Current computer engineering evolves at an accelerated pace, with hardware advancing towards new chip multiprocessors (CMP) architectures and with supporting software gearing towards new programming and abstraction paradigms, to obtain the maximum efficiency of the hardware at a low cost. In this context, Tilera Corporation has developed a brand new CMP architecture with 64 cores (tiles) called Tile64, and has launched several Peripheral Component Interconnect Express (PCIe) cards to be used and monitored from a host Personal Computer (PC). These cards may execute parallel applications built in C/C++ and compiled with the Tile-GCC compiler. We have previously demonstrated the usefulness of the Tile64 architecture for bioinformatics [S. Gálvez, D. Díaz, P. Hernández, F.J. Esteban, J.A. Caballero, G. Dorado, Next-generation bioinformatics: using many-core processor architecture to develop a web service for sequence alignment, Bioinformatics, 26 (2010) 683–686]. We have chosen a bioinformatics algorithm to test this many-core Tile64 architecture because of actual bioinformatics challenging needs: data-intensive workloads, space and time-consuming requirements and massive calculation. This algorithm, known as Needleman–Wunsch/Smith–Waterman (NW/SW), obtains an optimal sequence alignment in quadratic time and space cost, yet requires to be optimized to take full advantage of computing parallelization. In this paper we redesign, implement and fine-tune this algorithm, introducing key optimizations and changes that take advantage of specific Tile64 characteristics: RISC architecture, local tile’s cache, length of memory word, shared memory usage, RAM file system, tile’s intercommunication and job selection from a pool. The resulting algorithm – named MC64-NW/SW for Multicore64 Needleman–Wunsch/Smith–Waterman – achieves a gain of ∼1000% when compared with the same algorithm on a ×86 multi-core architecture. As far as we know, our NW/SW implementation is the fastest ever published for a standalone PC when aligning a pair of sequences larger than 20 kb.

Modeling sequence and function similarity between proteins for protein functional annotation.

A common task in biological research is to predict function for proteins by comparing sequences between proteins of known and unknown function. This is often done using pair-wise sequence alignment algorithms (e.g. BLAST). A problem with this approach is the assumption of a simple equivalence between a minimum sequence similarity threshold and the function similarity between proteins. This assumption is based on the binary concept of homology in that proteins are or not homologous. The relationship between sequence and function however is more complex as well as pertinent for predicting protein function, e.g. evaluating BLAST alignments or developing training sets for profile models based on functional rather than homologous groupings. Our motivation for this study was to model sequence and function similarity between proteins to gain insights into the "sequence-function similarity relationship between proteins for predicting function. Using our model we found that function similarity generally increases with sequence similarity but with a high degree of variability. This result has implications for pair-wise approaches in that it appears sequence similarity must be very high to ensure high function similarity. Profile models which enable higher sensitivity are a potential solution. However, multiple sequences alignments (a necessary prerequisite) are a problem in that current algorithms have difficulty aligning sequences with very low sequence similarity, which is common in our data set, or are intractable for high numbers of sequences. Given the importance of predicting protein function and the need for multiple sequence alignments, algorithms for accomplishing this task should be further refined and developed.

MTRAP: Pairwise sequence alignment algorithm by a new measure based on transition probability between two consecutive pairs of residues

BackgroundSequence alignment is one of the most important techniques to analyze biological systems. It is also true that the alignment is not complete and we have to develop it to look for more accurate method. In particular, an alignment for homologous sequences with low sequence similarity is not in satisfactory level. Usual methods for aligning protein sequences in recent years use a measure empirically determined. As an example, a measure is usually defined by a combination of two quantities (1) and (2) below: (1) the sum of substitutions between two residue segments, (2) the sum of gap penalties in insertion/deletion region. Such a measure is determined on the assumption that there is no an intersite correlation on the sequences. In this paper, we improve the alignment by taking the correlation of consecutive residues.ResultsWe introduced a new method of alignment, called MTRAP by introducing a metric defined on compound systems of two sequences. In the benchmark tests by PREFAB 4.0 and HOMSTRAD, our pairwise alignment method gives higher accuracy than other methods such as ClustalW2, TCoffee, MAFFT. Especially for the sequences with sequence identity less than 15%, our method improves the alignment accuracy significantly. Moreover, we also showed that our algorithm works well together with a consistency-based progressive multiple alignment by modifying the TCoffee to use our measure.ConclusionsWe indicated that our method leads to a significant increase in alignment accuracy compared with other methods. Our improvement is especially clear in low identity range of sequences. The source code is available at our web page, whose address is found in the section "Availability and requirements".

GR-Aligner: an algorithm for aligning pairwise genomic sequences containing rearrangement events

Homologous genomic sequences between species usually contain different rearrangement events. Whether some specific patterns existed in the breakpoint regions that caused such events to occur is still unclear. To resolve this question, it is necessary to determine the location of breakpoints at the nucleotide level. The availability of sequences near breakpoints would further facilitate the related studies. We thus need a tool that can identify breakpoints and align the neighboring sequences. Although local alignment tools can detect rearrangement events, they only report a set of discontinuous alignments, where the detailed alignments in the breakpoint regions are usually missing. Global alignment tools are even less appropriate for these tasks since most of them are designed to align the conserved regions between sequences in a consistent order, i.e. they do not consider rearrangement events. We propose an effective and efficient pairwise sequence alignment algorithm, called GR-Aligner (Genomic Rearrangement Aligner), which can find breakpoints of rearrangement events by integrating the forward and reverse alignments of the breakpoint regions flanked by homologously rearranged sequences. In addition, GR-Aligner also provides an option to view the alignments of sequences extended to the breakpoints. These outputs provide materials for studying possible evolutionary mechanisms and biological functionalities of the rearrangement.

A Parallel Pairwise Local Sequence Alignment Algorithm

Researchers are compelled to use heuristic-based pairwise sequence alignment tools instead of Smith-Waterman (SW) algorithm due to space and time constraints, thereby losing significant amount of sensitivity. Parallelization is a possible solution, though, till date, the parallelization is restricted to database searching through database fragmentation. In this paper, the power of a cluster computer is utilized for developing a parallel algorithm, RPAlign, involving, first, the detection of regions that are potentially alignable, followed by their actual alignment. RPAlign is found to reduce the timing requirement by a factor of upto 9 and 99 when used with the basic local alignment search tool (BLAST) and SW, respectively, while keeping the sensitivity similar to the corresponding method. For distantly related sequences, which remain undetected by BLAST, RPAlign with SW can be used. Again, for megabase-scale sequences, when SW becomes computationally intractable, the proposed method can still align them reasonably fast with high sensitivity.