Reducing storage requirements for biological sequence comparison
نویسندگان
چکیده
منابع مشابه
Reducing storage requirements for biological sequence comparison
MOTIVATION Comparison of nucleic acid and protein sequences is a fundamental tool of modern bioinformatics. A dominant method of such string matching is the 'seed-and-extend' approach, in which occurrences of short subsequences called 'seeds' are used to search for potentially longer matches in a large database of sequences. Each such potential match is then checked to see if it extends beyond ...
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Biological sequence comparison is a time consuming task on a Von Neuman computer. The addition of dedicated hardware for parallelizing the comparison algorithms results in a reduction of several orders of magnitude in the execution time. This paper presents and compares different dedicated approaches, based on the parallelization of the algorithms on linear arrays of processors.
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We have developed three computer programs for comparisons of protein and DNA sequences. They can be used to search sequence data bases, evaluate similarity scores, and identify periodic structures based on local sequence similarity. The FASTA program is a more sensitive derivative of the FASTP program, which can be used to search protein or DNA sequence data bases and can compare a protein sequ...
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MOTIVATION SAMBA (Systolic Accelerator for Molecular Biological Applications) is a 128 processor hardware accelerator for speeding up the sequence comparison process. The short-term objective is to provide a low-cost board to boost PC or workstation performance on this class of applications. This paper places SAMBA amongst other existing systems and highlights the original features. RESULTS R...
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ژورنال
عنوان ژورنال: Bioinformatics
سال: 2004
ISSN: 1367-4803,1460-2059
DOI: 10.1093/bioinformatics/bth408