Shouji: a fast and efficient pre-alignment filter for sequence alignment
نویسندگان
چکیده
منابع مشابه
Fast A Algorithms for Multiple Sequence Alignment
The multiple alignment of the sequences of DNA and proteins is applicable to various important elds in molecular biology. Although the approach based on Dynamic Programming is well-known for this problem, it requires enormous time and space to obtain the optimal alignment. On the other hand, this problem corresponds to the shortest path problem and the A algorithm, which can e ciently nd the sh...
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Sequence alignments are becoming more important with the increase of nucleic acid data. Fitch and Smith have recently given an example where multiple insertion/deletions (rather than a series of adjacent single insertion/deletions) are necessary to achieve the correct alignment. Multiple insertion/deletions are known to increase computation time from O(n2) to O(n3) although Gotoh has presented ...
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Analyzing and comparing the string representations of sequences reveals a lot of useful information about the sequences. As new biological sequences are being generated at exponential rates, sequence comparison is becoming increasingly important to draw functional and evolutionary inference of proteins. This paper presents a partitioning approach for biomolecular sequence alignment that signifi...
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Bioinformatics, through the sequencing of the full genomes for many species, is increasingly relying on efficient global alignment tools exhibiting both high sensitivity and specificity. Many computational algorithms have been applied for solving the sequence alignment problem. Dynamic programming, statistical methods, approximation and heuristic algorithms are the most common methods appli...
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Multiple sequence alignment has been a useful method in the study of molecular evolution and sequence-structure relationships. This paper presents a new method for multiple sequence alignment based on simulated annealing technique. Dynamic programming has been widely used to find an optimal alignment. However, dynamic programming has several limitations to obtain optimal alignment. It requires ...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2019
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/btz234