The terminology and notation used in this paper are introduced in the following papers: [22], [3], [20], [9], [5], [12], [10], [11], [15], [2], [18], [4], [1], [21], [16], [17], [14], [13], [19], [6], [7], and [8]. For simplicity, we follow the rules: X denotes a complex unitary space, s1, s2, s3 denote sequences of X, R1 denotes a sequence of real numbers, C1, C2, C3 denote complex sequences, ...

Sequence similarity/database searching is a cornerstone of molecular biology. PairsDB is a database intended to make exploring protein sequences and their similarity relationships quick and easy. Behind PairsDB is a comprehensive collection of protein sequences and BLAST and PSI-BLAST alignments between them. Instead of running BLAST or PSI-BLAST individually on each request, results are retrie...

We present a new method for multiple sequence alignment (MSA), which we call MSACSA. The method is based on the direct application of a global optimization method called the conformational space annealing (CSA) to a consistency-based score function constructed from pairwise sequence alignments between constituting sequences. We applied MSACSA to two MSA databases, the 82 families from the BAliB...

The sequence alignment is a fundamental problem in computational biology. Many sequence alignment methods have been proposed, such as pair-wise sequence alignment, multiple sequence alignment (MSA), syntenic alignment, constraint multiple sequence alignment, and etc. Among them, pair-wise sequence alignment is a most commonly used method. Recently, MSA is more and more important which has been ...

The search for novel proteins is complicated by the diversity of amino acids, the non-linear relationship between amino acid sequence and folding and the huge size of sequence space. The goal of this research is to discover patterns in amino acid composition and sequence that relate to known or novel folds, thereby helping to constrain the search space for new functional proteins. This approach...

This paper introduces a method for quantization of image-sequences which takes into account the human sensitivities in both space and time. A weighted clustering approach is used for quantization which allows exibility in the choice of weights. Assigning weights proportional to the space gradients and the time gradients is shown to produce better quantization of color image sequences.

Sequence comparison with affine gap costs is a problem that is readily parallelizable on simple single-instruction, multiple-data stream (SIMD) parallel processors using only constant space per processing element. Unfortunately, the twin problem of sequence alignment, finding the optimal character-by-character correspondence between two sequences, is more complicated. While the innovative O(n2)...