Abstract Trev is a DNA trace editor and viewer, which is available free for UNIX and Microsoft Windows platforms. It can read all the commonly used file formats, including the new, compact ZTR files. Availability: ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/trev Contact: [email protected] * To whom correspondence should be addressed.

Abstract Motivation: To produce an open and extensible file format for DNA trace data which produces compact files suitable for large-scale storage and efficient use of internet bandwidth. Results: We have created an extensible format named ZTR. For a set of data taken from an ABI-3700 the ZTR format produces trace files which require 61.6% of the disk space used by gzipped SCFv3, and which can be written and read at greater speed. The compression algorithms used for the trace amplitudes are used within the National Center for Biotechnology Information (NCBI) trace archive. Availability: Source code is available from ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/io_lib/io_lib.tar.gz. A complete format description can be found at http://www.mrc-lmb.cam.ac.uk/pubseq/ztr.html. Test data is available from ftp://ftp.mrc-lmb.cam.ac.uk/pub/staden/io_lib/test_data. Contact: [email protected] * To whom correspondence should be addressed.

Tim J. Gleeson, Rodger Staden; An X windows and UNIX implementation of our sequence analysis package, Bioinformatics, Volume 7, Issue 3, 1 July 1991, Pages 398,

We report improvements to our sequence analysis package and adaptation to run on the Apple Macintosh range of machines. The 'standard' version of the programs, which run on a VAX, has been given a new user interface that makes the programs very much easier to work with and has facilitated the move to the Macintosh. The reorganization of the code should simplify moves to other systems that offer WIMP user interfaces. In addition to a large number of small but useful extra features, some important new analytical functions have been devised. These include sequence and contig editors; optimal alignment and comparison methods; and a new method for comparing the observed and expected frequencies of selected oligonucleotides.

This paper describes the use of probability-generating functions for calculating the probabilities of finding motifs in nucleic acid and protein sequences. Equations and algorithms are given for calculating the probabilities associated with nine different ways of defining motifs. Comparisons are made with searches of random sequences. A higher level structure--the pattern--is defined as a list of motifs. A pattern also specifies the permitted ranges of spacing allowed between its constituent motifs. Equations for calculating the expected numbers of matches to patterns are given.

We describe a computer tool to aid the discovery of new motifs in nucleic acid sequences. A typical use would be to analyse a set of upstream regions from a family of related genes in order to find possible control sequences. The heart of the method is the creation of dictionaries of related subsequences. These dictionaries can then be analysed to look for the commonest or best-defined subsequences, those that occur in the highest number of different sequences, or for those in equivalent positions within the family. We show the application of the method to a set of E. coli promoter sequences.

A method to define and search for complex patterns of motifs in nucleic acid and protein sequences is described. With this method nucleic acid motifs can be defined in eight different ways and protein motifs in six. A pattern is defined by a list of motifs. The motifs in a list are combined using the logical operators AND, OR and NOT. The list also defines the ranges of allowed separations of the motifs in the pattern. Programs to search for patterns in individual sequences and libraries of sequences are described. Patterns are defined by users and stored as annotated disk files. Hence the programming to define and locate new structures can be performed by users and fewer specific novel algorithms should be required. Examples are given of searches for transcription initiation regions, nematode mitochondrial tRNA genes and for members of the globin sequence family.

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.