Sequence allignment tools

Additionally, our Sequence Alignment tool utilizes gaps and gap penalties while aligning the two sequences to maximize the chances of matching two nucleotides or two amino acids while maintaining data integrity. While gaps account for insertions or deletions in the aligned sequences, gap penalties assign negative scores to the alignment based on the frequency and length of the gaps.

Login or Register. Local alignment tools find one, or more, alignments describing the most similar region s within the sequences to be aligned.

They are can align protein and nucleotide sequences. Genomic alignment tools concentrate on DNA or to DNA alignments while accounting for characteristics present in genomic data. Introduction Next generation sequencers NGS have increased the amount of data obtainable by genome sequencing; a NGS run produces millions of short sequences, called reads , that is, a sequence of nucleotides containing also information about the quality of the sequencing process, which determine the reliability of the nucleotide called during sequencing.

Related Works Many algorithms for sequence alignment have been proposed and different tools were implemented that entirely exploit multithreading on homogeneous and heterogeneous platforms. Alignment Tools The first step done before an alignment is to create and load the reference genome.

Tools Parallelisation and Optimisations Alignment tools, generally, exploit parallelism via multithreading. Datasets There exist several technologies for DNA sequencing, which produce reads of different lengths. Materials and Methods 3. Open in a separate window. Figure 1. The Paradigmatic Structure of Parallel Alignment Tools As discussed in related works Section 2 , a plethora of sequence alignment tools is currently available. As a matter of fact, all the most popular parallel alignment tools, including Bowtie2, BWA, and BLASR, implement a master-worker paradigm, where each worker cycles over the following three steps: gets a sequence to align from the shared input file; aligns the read against the genome loaded into the shared index file; populates shared data structures with results and statistics.

Case Studies 3. Bowtie The Bowtie2 a. Figure 2. Roche and Illumina Datasets Within this work, we aligned datasets obtained with three different sequencing technologies in order to show how they behave with various lengths. Table 1 Datasets. PacBio 55—6, , Figure 3. Figure 4. Figure 5. Performance Comparison and Analysis In this section, the original multithreaded implementation of Bowtie and BWA alignment tools are compared for performance to their porting onto the FastFlow pattern-based library on different datasets.

Table 3 Alignment tools key. Acronym Tool Version Variant Technology bt Figure 6. Figure 7. PacBio Human Datasets Performances of bt Table 4 Bt Figure 8. Metric bt Performance Analysis Further information to explain performance differences of the different versions of Bowtie2 can be extracted via perf , a performance analyser tool in Linux.

Testing on an Alternative Platform To assess results across different platforms, the tools were tested also on a different platform, an Intel Sandy Bridge with two 8-core sockets 2 HyperThreads 2. Figure 9. Figure Conclusions In this paper, we analysed the problem of sequence alignment from parallel computing perspective; we reviewed the design of three of the most popular alignment tools exhibiting parallel computing capabilities, among others, Bowtie2, BWA, and BLASR.

Conflict of Interests The authors declare that there is no conflict of interests regarding the publication of this paper. References 1. Cole M. Pitman: Research Monographs in Parallel and Distributed Computing. Aldinucci M, Danelutto M. Stream parallel skeleton optimization. ACTA Press; pp. Fastflow: high-level and efficient streaming on multi-core. In: Pllana S, Xhafa F, editors.

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