The FASTA package of sequence comparison programs has been modified to provide accurate statistical estimates for local sequence similarity scores with gaps. These estimates are derived using the extreme value distribution from the mean and variance of the local similarity scores of unrelated sequences after the scores have been corrected for the expected effect of library sequence length. This...

Efficient sequence alignment is one of the most important and challenging activities in bioinformatics. Many algorithms have been proposed to perform and accelerate sequence alignment activities. Among them SmithWaterman (S-W) is the most sensitive (accurate) algorithm, however, the fact that it is the most computationally intensive algorithm makes it necessary to implement hardware acceleratio...

In this paper, we establish Lp norm bounds for spectral clusters on compact manifolds, under the assumption that the metric is C1,1. Precisely, we show that the Lp estimates proven by Sogge in the case of smooth metrics hold under this limited regularity assumption. It is known by examples of Smith-Sogge that such estimates fail for C1,α metrics if α < 1.

PARALIGN is a rapid and sensitive similarity search tool for the identification of distantly related sequences in both nucleotide and amino acid sequence databases. Two algorithms are implemented, accelerated Smith-Waterman and ParAlign. The ParAlign algorithm is similar to Smith-Waterman in sensitivity, while as quick as BLAST for protein searches. A form of parallel computing technology known...

Using data from the CATH structure classification, we have assessed the blastp, fasta, smith-waterman and gapped-blast algorithms, developed a portable normalization scheme and identified safe thresholds for database searching. Of the four methods assessed, fasta, smith-waterman and gapped-blast perform similarly, whereas the sensitivity of blastp was much lower. Introduction of an intermediate...

Analyses of phase transitions in biopolymers have previously been restricted to studies of average behavior along macromolecules. Extremal properties, such as longest helical region, can now be studied with a new family of probability distributions [Arratia, R., Gordon, L. & Waterman, M. S. (1986) Ann. Stat. 14, 971-993]. Not only is such extremal behavior analyzed with great precision, but new...

Some of the leading models and frameworks about Excellence from the last 25 years are presented and discussed: Peters and Waterman’s eight excellence attributes (1982), Peters and Austin’s simplified excellence model (1985), Lists of Best Practices, Xerox Excellence Models (1990, 2002), the European Excellence Model (1992) and two different but overlapping “4P Models” (1999, 2004). At the end o...

A number of models about identity development have been proposed based on Erikson’s theory such as Marcia’s (1966) Identity Status Model, Waterman’s (1992) Optimal Psychological Functioning Model and Berzonky’s (1992) Identity Styles Model. Marcia’s Identity Status Model is the model most frequently used in studies. Marcia (1966; 1989; 1994; 2002) defined four identity statuses based on explora...