The Sequence Motif Analysis and Retrieval Tool (SMART) is a computer program package that searches sequence motifs in a query protein sequence and gives additional information of structural and functional features about the detected motifs. These features are represented in a graphical fashion, and for structural features, users can manipulate the three-dimensional structures containing the detected motifs using a graphical user interface. SMART aims at providing more useful information for interpreting biological functions of the query sequence than a simple database retrieval of homology searches. SMART works on Sun workstations with an X windows graphical user interface system.

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We have developed an alignment editor for protein sequences and/or nucleotide sequences that runs under the on X-window system. The system is equipped with automatical aligner and motif dictionary. The system can iteratively identify known motifs stored in the motif dictionary and gradually improve the quality of the alignment to discover new motifs.

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We developed a new computer language that describes three-dimensional graphical objects for visual simulation. The language, 3D-Talk, is a powerful means for visualizing the process of protein folding simulation. 3D-Talk is designed as an object-oriented language, with which users can create, manipulate, and edit graphical objects using commands with a syntax like a natural language.
We developed two novel applications for molecular biology using 3D-Talk. One is ProView, a protein visualization tool. ProViewconverts the data of PDB (Protein Data Bank) into 3D-Talk statement. Another is a visual simulation system for protein folding. It simulates the motion of protein folding using simulated annealing techniques and Hidden Markov Models.
In short, 3D-Talk serves as a powerful animation tool.

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We have been developing an interactive database system for three dimensional protein structures named PROTEIX. The most important feature of PROTEIX is that it has pattern matching facilities for three dimensional protein structures. For example, such functions as substructure search and alignment of two protein structures are included. As well as such functions, PROTEIX has the following facilities: a mechanism for inputing a file in PDB (Protein Data Bank) data format, an interactive graphic interface, and various pattern matching functions for amino acid sequences (strings).
Currently, PROTEIX is being developed and is used as a workbench for developing pattern matching algorithms. The final target of the system is to be a prototype of a powerful tool for biologists who study relations between amino acid sequences and three dimensional structures of proteins. PROTEIX is implemented on UNIX workstations using C-language. X-window is adopted for the graphic interface.

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Three modules of a computer system for predicting membrane protein structure have been developed. First module distinguishes membrane proteins from other type of proteins based upon the information of amino acid sequence alone. In this process, only hydrophobicity of amino acids has been used and the discrimination of 99% was possible, analyzing amino acid sequence by Fourier transform method. The secondary structure is predicted in the second module, in which the hydrophobicity played dominant role. The last module predicts the configuration of transmembrane helices solving a jigsaw puzzle, the pieces of which are rods of helices with polar areas on their surface.

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We have been compiled knowledge libraries of proteins for anonymous FTP site on genome network. The libraries are asite, bsite, corn, horn, mot, mut, oligo, per, ster, top and xray. These libraries include reference list containing sequence-related knowledges and the references are extracted from literature databa.se (LITDB). Each library contains data in the format: one line for one record and each item is delimited by character “:”. Information in each library are as follows. asite: active site, bsite: binding site, com: conserved sequence, horn: homologous proteins, mot: motif sequences, mut: mutant proteins, oligo: oligonucleotide probe sequences for sequencing proteins, per: primer sequences for polymerase chain reaction, ster: references of stereo drawing, top: topics for proteins, xray: references of x-ray analysis of proteins. We show some example how to use these library with the UNIX commands: grep, sed, awk, sort, head etc.

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National Cancer Center Research Institute has about 200 researchers. Most of them are engaged in studies of molecular biology. Before the introduction of Local Area Network system (LAN), each division in our institute had their own genetic analysis system working independently. As we integrated LAN and connected it to the internet by joining TISN, we planned to make a total system for genetic analysis. Our concept was to make a system so that all researchers can use updated versions of database and analyze their data by supercomputers, easily. We thought it is hard for all researchers to use UNIX commands to perform their searches and retrievals to the database. So, our system is consisted with PC-9801 or Macintosh based system. It uses daily-updated database from NCBI to search by PC-9801 or macintosh programs. It includes gopher system to retrieve required sequence from database, and connection to mail-servers at many places to perform homology searches using supercomputers. As we are maintaining a gopher server in our institute, we are now making a gopher interface to many databases to retrieve and search data easily. We are performing many services not only to the researchers in our institute but also to the researchers outside our institute.

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Genome research has been (and will be) producing information about genes including structures and genetic loci as well as their products, functions, information as markers, and phenotypic effects. All of these are stored separately or combined through several databases. In addition, information on genetic markers, STSs, contigs, and chromosomal abnormalities are also included in the storage. Out of these, our major interest is information relating to human genes. Structures and functions of the genes and their products, regulation mechanisms, for example, during development, relation with known disorders will provide essential clue to understand function of life. In this study, a database focused on human genes has been designed and the prototype has been constructed. Main purpose of the database is to create generic collection of data on human genes. Such database should be tailored for the majority of the users, the Biologists, to reduce complications required when fishing for necessary data going through different databases. At present, portion of GDB/OMIM, DDBJ/EMBL/GenBank, and PIR/SWISSPROT databases are extracted and stored in a Macintosh computer.

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The enormous amount of data that is provided by the genome sequencing projects around the world poses a great challenge to science, namely, to decode and interpret these data. There are different aspects to this problem, such as
. resolving the three-dimensional conformation of proteins and nucleic acids known by their sequence,
. uncovering the mechansims underlying the biological function of molecules such as proteins and nucleic acids,
. gaining insights into the role of non-coding stretches of DNA.
Advances in computing technology encourage us, to approach some of these questions with the aid of the computer. Due to the dramatic increase in computing power and, in particular, due to the newly gained graphics capabilities, we can visualize structure as well as dynamics of biopolymers on the computer screen. What is still largely missing is a set of reliable models and algorithmic methods for inferring molecular conformation on the basis of sequence knowledge and for reliably predicting the chemical interactions among macromolecules and between macromolecules and smaller ligands.
In this talk, we want to address a number of problems, whose solution requires algorithmic research as an essential ingredient. As a result, cooperation with computer scientists may be a promising approach to solving these problems. In response to this challenge, the German science ministry has started a research initiative entitled “molecular bioinformatics” that supports interdisciplinary research in this area incorporating molecular biologists and computer scientists over a period of four years.
We plan to give a general overview over a whole set of problem areas in the field of molecular bioinformatics and then focus on problems in the areas of homology-based modelling and docking.

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First, a brief overview of genome informatics work at Los Alamos will be given. This will describe (1) the Los Alamos Sequence Database, (2) the AIDS Database, (3) theoretical design for genome mapping, (4) map assembly tools and methods, (5) a shotgun sequencing assembly algorithm, (6) studies in the evolution of repeats, (7) work on genome organization and estimation of genome coding density, and (8) gene identification methods.
Second, more technical depth will be given on one topic, that of gene identification. The state of the art (worldwide) will be described for the problem of computationally identifying genes in eukaryotic DNA. The component techniques used in gene identification algorithms (measurement of statistical regularities, identification of transcription and translation signals, and matching to overall gene syntax) will be described, then the synergy that results when different component techniques are combined, and finally the integrated algorithms of (1) Fields and Soderlund, (2) Guigo' et al., (3) Gelfand, and (4) Snyder and Stormo.
Although it is impossible to describe in detail all currently available tools, enough of the leading tools will be described to give a clear understanding of what capabilities are now available. In addition, since no existing tool combines all of the best available techniques, techniques will be reviewed in a more abstract sense, with the goal of clarifying where current algorithms are being improved, and how much performance is likely to progress in the near future.

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