the sequences and e ciently answer similarity queries. We provide experimental results which show that our method is superior to search based on sequential scanning. Our experiments show that a few coefficients (1-3) are adequate to provide good performance. The performance gain of our method increases

A method to correlate the uninterpreted tandem mass spectra of peptides produced under low energy (lo-50 eV) collision conditions with amino acid sequences in the Genpept database has been developed. In this method the protein database is searched to identify linear amino acid sequences within a

relationships; the third, fold, describes geometrical relationships. The distinction between evolutionary relationships and those that arise from the physics and chemistry of proteins is a feature that is unique to this database, so far. The database can be used as a source of data to calibrate sequence search

ABSTRACT The BLAST programs are widely used tools for searching protein and DNA databases for sequence similarities. For protein comparisons, a variety of definitional, algorithmic and statistical refinements described here permits the execution time of the BLAST programs to be decreased

Hidden.Markov Models (HMMs) are applied t.0 the problems of statistical modeling, database searching and multiple sequence alignment of protein families and protein domains. These methods are demonstrated the on globin family, the protein kinase catalytic domain, and the EF-hand calcium binding

We describe the Photobook system, which is a set of interactive tools for browsing and searching images and image sequences. These query tools differ from those used in standard image databases in that they make direct use of the image content rather than relying on text annotations. Direct search

A two-process theory of human information processing is proposed and applied to detection, search, and attention phenomena. Automatic processing is activa-tion of a learned sequence of elements in long-term memory that is initiated by appropriate inputs and then proceeds automatically

together can be used as a Bayes-optimal classifier for searching for occurrences of the motif in other databases. The algorithm estimates how many times each motif occurs in each sequence in the dataset and outputs an alignment of the occurrences of the motif. The algorithm is capable of discovering

of individuals. Results: We implemented BWA, a new read alignment package that is based on backward search with Burrows-Wheeler Transform (BWT), to efficiently align short sequencing reads against a large reference sequence such as the human genome, allowing mismatches and gaps. BWA supports both base space

. In this program, various methods for estimating evolutionary distances from nucleotide and amino acid sequence data, three different methods of phylogenetic inference (UPGMA, neighbor-joining and maximum parsimony) and two statistical tests of topological differences are included. For the maximum parsimony method