16 papers · ranked by Valyu relevance
Andrzej Zielezinski, Susana Vinga, Jonas Almeida, Wojciech M. Karlowski
'Wojciech M. Karlowski'] Alignment-free sequence analyses have been applied to problems ranging from whole-genome phylogeny to the classification of protein families, identification of horizontally transferred genes, and detection of recombined sequences. The strength of these methods makes them particularly useful for…
Jiannan Chao, Furong Tang, Lei Xu, Lukasz Kurgan
The continuous development of sequencing technologies has enabled researchers to obtain large amounts of biological sequence data, and this has resulted in increasing demands for software that can perform sequence alignment fast and accurately. A number of algorithms and tools for sequence alignment have been designed…
K.S Kong, E.Y.K Ng
The work showed that the integrated suite of software tools for detecting criminals using DNA databases has achieved the overall objective by providing a working platform for sequence analysis. The work also demonstrated that by integrating BLAST and FASTA (two widely used and freely available algorithms), plus an…
Paul A Gagniuc, Elvira Gagniuc
Sequence alignment provides a formal framework for comparison of biological sequences through score maximization over matches, mismatches, and insertion-deletion events. Classical formulations distinguish between global alignment, which enforces end-to-end correspondence through fixed boundary conditions, and local…
Ken D Nguyen, Yi Pan, Ge Nong
Background One of the most fundamental and challenging tasks in bio-informatics is to identify related sequences and their hidden biological significance. The most popular and proven best practice method to accomplish this task is aligning multiple sequences together. However, multiple sequence alignment is a computing…
Manish Kumar
One of the most fundamental operations in biological sequence analysis is multiple sequence alignment (MSA). The basic of multiple sequence alignment problems is to determine the most biologically plausible alignments of protein or DNA sequences. In this paper, an alignment method using genetic algorithm for multiple…
Minh Duc Cao, Trevor I Dix, Lloyd Allison
Background Traditional genome alignment methods consider sequence alignment as a variation of the string edit distance problem, and perform alignment by matching characters of the two sequences. They are often computationally expensive and unable to deal with low information regions. Furthermore, they lack a…
Gayathri Jayaraman, Rahul Siddharthan
Background While most multiple sequence alignment programs expect that all or most of their input is known to be homologous, and penalise insertions and deletions, this is not a reasonable assumption for non-coding DNA, which is much less strongly conserved than protein-coding genes. Arguing that the goal of sequence…
Arash Bayat, Bruno Gaëta, Aleksandar Ignjatovic, Sri Parameswaran
Background Pairwise alignment of short DNA sequences with affine-gap scoring is a common processing step performed in a range of bioinformatics analyses. Dynamic programming (i.e. Smith-Waterman algorithm) is widely used for this purpose. Despite using data level parallelisation, pairwise alignment consumes much time.…
Veska Gancheva, Hristo Stoev, Clifford J. Steer
Bioinformatics is a rapidly developing field enabling scientific experiments via computer models and simulations. In recent years, there has been an extraordinary growth in biological databases. Therefore, it is extremely important to propose effective methods and algorithms for the fast and accurate processing of…
Orion Penner, Peter Grassberger, Maya Paczuski, Konrad Scheffler
Background Existing sequence alignment algorithms use heuristic scoring schemes based on biological expertise, which cannot be used as objective distance metrics. As a result one relies on crude measures, like the p- or log-det distances, or makes explicit, and often too simplistic, a priori assumptions about sequence…
Dimitrios P Lyras, Dirk Metzler
Background Obtaining an accurate sequence alignment is fundamental for consistently analyzing biological data. Although this problem may be efficiently solved when only two sequences are considered, the exact inference of the optimal alignment easily gets computationally intractable for the multiple sequence alignment…
Saikat Chakrabarti, Nitin Bhardwaj, Prem A Anand, Ramanathan Sowdhamini
'Ramanathan Sowdhamini'] Background Multiple sequence alignment algorithms are very important tools in molecular biology today. Accurate alignment of proteins is central to several areas such as homology modelling, docking studies, understanding evolutionary trends and study of structure-function relationships. In…
Lorraine A. K. Ayad, Solon P. Pissis
Background A fundamental assumption of all widely-used multiple sequence alignment techniques is that the left- and right-most positions of the input sequences are relevant to the alignment. However, the position where a sequence starts or ends can be totally arbitrary due to a number of reasons: arbitrariness in the…
Rahul Siddharthan
Background Existing tools for multiple-sequence alignment focus on aligning protein sequence or protein-coding DNA sequence, and are often based on extensions to Needleman-Wunsch-like pairwise alignment methods. We introduce a new tool, Sigma, with a new algorithm and scoring scheme designed specifically for non-coding…
Kieran Boyce, Fabian Sievers, Desmond G. Higgins
Background Progressive alignment is the standard approach used to align large numbers of sequences. As with all heuristics, this involves a tradeoff between alignment accuracy and computation time. Results We examine this tradeoff and find that, because of a loss of information in the early steps of the approach, the…