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Finding anchors for genomic sequence comparison
Proceedings of the eighth annual international conference on Computational molecular biology - RECOMB '04, 2004Recent sequencing of the human and other mammalian genomes has brought about the necessity to align them, to identify and characterize their commonalities and differences. Programs that align whole genomes generally use a seed-and-extend technique, starting from exact or near-exact matches and selecting a reliable subset of these, called anchors, and ...
Ross Lippert +4 more
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Sequence Comparison Among Arenaviruses
1987Contemporary techniques for DNA cloning and rapid nucleotide sequencing have made significant contributions to the present understanding of gene structure and regulation (see, for example, Gluzman and Shenk 1983; Gluzman 1985). Cloning has allowed the amplification of genetic material that may be difficult or impossible to propagate by conventional ...
P J, Southern, D H, Bishop
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A sequence-comparison statistic and algorithm
Biometrika, 1973SUMMARY A statistic is proposed for the comparison of ordered sequences of objects when the aim is to slot together the sequences. An algorithm is suggested for attempting to find the best pairwise fit. A fair number of problems in the earth and life sciences can be regarded in terms of comparing ordered sequences of objects.
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Parallel sequence comparison and alignment
Proceedings The International Conference on Application Specific Array Processors, 2002Sequence comparisons, a vital research tool in computational biology, is based on a simple O(n/sup 2/) algorithm that easily maps to a linear array of processors. This paper reviews and compares high-performance sequence analysis on general-purpose supercomputers and single-purpose, reconfigurable, and programmable co-processors.
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Secure and Efficient Outsourcing of Sequence Comparisons
2012We treat the problem of secure outsourcing of sequence comparisons by a client to remote servers, which given two strings λ and μ of respective lengths n and m, consists of finding a minimum-cost sequence of insertions, deletions, and substitutions (also called an edit script) that transform λ into μ. In our setting a client owns λ and μ and outsources
Marina Blanton +3 more
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Comparison of Symbol Sequences: No Editing, No Alignment
Open Systems & Information Dynamics, 2002The new method to compare two (or several) symbol sequences is developed. The method is based on the comparison of the frequencies of the small fragments of the compared sequences; it requires no string editing or other transformations of the compared objects.
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Fast Comparison of a DNA Sequence with a Protein Sequence Database
Microbial & Comparative Genomics, 1996We describe a computer program, named DNA-Protein Search (DPS), for comparing a megabase DNA sequence with a protein sequence database. The DPS program addresses the problems of frameshifts and introns in the DNA sequence. The DPS program was used to compare each of the following sequences with the Swiss-Prot database: the 1.8 ...
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Protein sequence comparisons: searching databases and aligning sequences
Current Opinion in Biotechnology, 1994As the explosive growth of sequence databases continues, both the content of these databases and the best strategies for exploiting them are changing. Remarkable improvements in the performance of microcomputers have put very sophisticated tools within the reach of all investigators.
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