The European Molecular Biology Open Software Suite ( EMBOSSEMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. The software automatically copes with data in a variety of formats and even allows transparent retrieval of sequence data from the web. Also, as extensive libraries are provided with the package, it is a platform to allow other scientists to develop and release software in true open source spirit. EMBOSS also integrates a range of currently available packages and tools for sequence analysis into a seamless whole. EMBOSS breaks the historical trend towards commercial software packages.EMBnethistorical

EMBOSS has several important advantages: It is free as in 'no charge'. It is free as in 'free speech'. It runs on practically every UNIX you can think of and some that you can't - plus MacOSs. It provides a comprehensive set of sequence analysis programs (approximately 100). It handles all sequence and many sequence alignment and structure formats. It integrates other publicly available packages. Encourages the use of EMBOSS in sequence analysis training. Encourages developers elsewhere to use the EMBOSS libraries. It is free of arbitrary size limits - notoriously difficult memory management in C is handled by the system, not the programmer, and memory for sequences or matrices is allocated dynamically; the only restriction is the hardware. It contains library functions for general string handling, pattern-matching, sorting, iteration and (imminently) extremely fast indexing. It contains library functions for all common sequence analysis tasks. It has a consistent API for interface designers to program to.

ALIGNMENT CONSENSUS DIFFERENCES DOT PLOTS GLOBAL LOCAL MULTIPLE DISPLAY EDIT ENZYME KINETICS FEATURE TABLES INFORMATION The programs are grouped by function NUCLEIC 2D STRUCTURE CODON USAGE COMPOSITION CPG ISLANDS GENE FINDING MOTIFS MUTATION PRIMERS PROFILES REPEATS RESTRICTION TRANSCRIPTION TRANSLATION PHYLOGENY PROTEIN 2D STRUCTURE 3D STRUCTURE COMPOSITION MOTIFS MUTATION PROFILES UTILS DATABASE CREATION DATABASE INDEXING MISC EMBOSS-GCG comparison

( Jemboss is developed at the HGMP-RC.HGMP-RC The software is free and part of the EMBOSS distribution. UK Human Genome Mapping Project Resource Centre Funded by the MRC Jemboss is a java based interface to EMBOSS. It provides the advantage of being able to provide sensible EMBOSS defaults on- the-fly for a given sequence or for a given input parameter. Jemboss can run the EMBOSS applications interactively or as a batch process. The progress of the batch processes are monitored by a job manager. Jemboss provides file managers for data transfer between the local machine and the remote machine that runs the EMBOSS applications. Local and remote files can be used in Jemboss. There is also a project manager responsible for maintaining the details of each run and the input and output files. These can be called up at any time and deleted by the user. The user can also add notes for each run.

Introduction to Sequence Analysis using EMBOSS