High-Performance Direct Pairwise Comparison of Large Genomic Sequences

Pairwise Comparison Between Genomic Sequences and Optical-maps

With the development and improvement of high throughput experimental technologies, massive amount of biological data including genomic sequences and optical-maps have been collected for various species. Comparative techniques play a central role in investigating the adaptive significance of organismal traits and revealing evolutionary relations among organisms by comparing these biological data...

Improving pairwise comparison of protein sequences with domain co-occurrence

Comparing and aligning protein sequences is an essential task in bioinformatics. More specifically, local alignment tools like BLAST are widely used for identifying conserved protein sub-sequences, which likely correspond to protein domains or functional motifs. However, to limit the number of false positives, these tools are used with stringent sequence-similarity thresholds and hence can miss...

High performance computation for direct numerical and large eddy simulation

This paper focusses on high order compact schemes for direct numerical simulation (dns) and large eddy simulation (les) for flow separation, transition, tip vortex, and flow control. We discuss the fundamental issues of high quality grid generation, high order schemes for curvilinear coordinates, the cfl condition for complex geometry, and high-order weighted compact schemes for shock capturing...

On inconsistency of a pairwise comparison matrix

Pairwise-nonrecurrent sequences

A new class of integer sequences is introduced in which any pair of identical symbols in the sequence, separated a certain number of digits apart, appears in the sequence, with that separation, at most once. For any given sequence length n and number of distinct symbols used, m, such a sequence, if it exists, is not unique; our attention is thus focused on the lexographically first such sequenc...