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Background: We present a novel method to encode ambiguously aligned regions in fixed multiple sequence alignments by ‘Pairwise Identity and Cost Scores Ordination’ (PICS-Ord)....
Robert K. Luecking, Brendan P. Hodkinson, Alexandr...
Background: Traditional genome alignment methods consider sequence alignment as a variation of the string edit distance problem, and perform alignment by matching characters of th...
The Smith-Waterman (SW) algorithm is one of the widely used algorithms for sequence alignment in computational biology. With the growing size of the sequence database, there is alw...
Abstract--We present a method for improving existing statistical machine translation methods using an knowledge-base compiled from a bilingual corpus as well as sequence alignment ...
— We present efficient cache-oblivious algorithms for some well-studied string problems in bioinformatics including the longest common subsequence, global pairwise sequence alig...
Rezaul Alam Chowdhury, Hai-son Le, Vijaya Ramachan...
—The most pervasive compute operation carried out in almost all bioinformatics applications is pairwise sequence homology detection (or sequence alignment). Due to exponentially ...
We study the problem of similarity detection by sequence alignment with gaps, using a recently established theoretical framework based on the morphology of alignment paths. Alignm...
Background: Parallel computing is frequently used to speed up computationally expensive tasks in Bioinformatics. Results: Herein, a parallel version of the multi-alignment program...
Martin Schmollinger, Kay Nieselt, Michael Kaufmann...
In this paper, we address the problem of multiple sequence alignment (MSA) for handling very large number of proteins sequences on mesh-based multiprocessor architectures. As the ...
Diana H. P. Low, Bharadwaj Veeravalli, David A. Ba...
Background: Exhaustive methods of sequence alignment are accurate but slow, whereas heuristic approaches run quickly, but their complexity makes them more difficult to implement. ...