Artemis: sequence visualization and annotation.

SUMMARY: Artemis is a DNA sequence visualization and annotation tool that allows the results of any analysis or sets of analyses to be viewed in the context of the sequence and its six-frame translation. Artemis is especially useful in analysing the compact genomes of bacteria, archaea and lower eukaryotes, and will cope with sequences of any size from small genes to whole genomes. It is implemented in Java, and can be run on any suitable platform. Sequences and annotation can be read and written directly in EMBL, GenBank and GFF format. AVAILABITLTY: Artemis is available under the GNU General Public License from http://www.sanger.ac.uk/Software/Artemis

The nucleotide sequence of Saccharomyces cerevisiae chromosome IX.

Large-scale systematic sequencing has generally depended on the availability of an ordered library of large-insert bacterial or viral genomic clones for the organism under study. The generation of these large insert libraries, and the location of each clone on a genome map, is a laborious and time-consuming process. In an effort to overcome these problems, several groups have successfully demonstrated the viability of the whole-genome random 'shotgun' method in large-scale sequencing of both viruses and prokaryotes. Here we report the sequence of Saccharomyces cerevisiae chromosome IX, determined in part by a whole-chromosome 'shotgun', and describe the particular difficulties encountered in the random 'shotgun' sequencing of an entire eukaryotic chromosome. Analysis of this sequence shows that chromosome IX contains 221 open reading frames (ORFs), of which approximately 30% have been sequenced previously. This chromosome shows features typical of a small Saccharomyces cerevisiae chromosome.

Image analysis of restriction enzyme fingerprint autoradiograms.

A genome mapping system has been developed that reads and assembles data from clones analysed by restriction enzyme fragmentation and polyacrylamide gel electrophoresis. Input data for the system can be most effectively obtained by the use of a scanning densitometer and image-processing package, such as that described in this article. The image-processing procedure involves preliminary location of bands, cooperative tracking of lanes by correlation of adjacent bands, a precise densitometric pass, alignment of the marker bands with the standard, optional interactive editing, and normalization of the accepted bands.

Data compression: 8-dimensional flow cytometric data processing with 28K addressable computer memory.

A method of data analysis for flow cytometry is presented which enables up to eight-dimensional data to be handled by a microcomputer with 28K addressable plus a further 32K non-addressable memory. The multi-parameter coordinates are coded into single numbers using a minimal modification of the array vector mapping equation. These code numbers, each of which corresponds to a given set of coordinates, and then ranked in ascending order according to magnitude and the frequency of each code number is found. Following this step the code is then decoded by integer arithmetic into its original coordinates which are then packed, together with the frequency, into two, three or four 16-bit words depending on the dimensionality of the data set. A five-dimensional data set is used as the illustration. Three regions were set on one two-dimensional data space and the five mono-dimensional histograms, plus a different bivariate distribution, were extracted in a single pass through the processed data file. In addition to considerable space saving the technique has two further attributes, namely, increased speed with which the user can appreciate multiparameter data and the ability to analyse such data sets with a microcomputer.

Software for genome mapping by fingerprinting techniques.

A genome mapping package has been developed for reading and assembling data from clones analysed by restriction enzyme fragmentation and polyacrylamide gel electrophoresis. The package comprises: data entry; matching; assembly; statistical analysis; modelling. Data entry can be either manual or by a semiautomatic system based on a scanning densitometer. The primary emphasis in the analytical routines is on flexibility and interactive convenience, so that the operator has full knowledge of and control over the growing map, but a variety of automatic options are included. The package continually grows to meet the needs of the Caenorhabditis project.