EMBOSS, and thus your BioBind installation, currently consists of 201 applications. These may be used alone or in conjuction with one another to assist in the computational analysis of biological problems.

There are 22 applications that can be applied to the alignment of two or more sequences. In addition to applications for creating alignments, such as dot plots, local, global and multiple alignment there are a variety of programmes for determining consensus and variation within existing alignments.

61 applications have been written with the purpose of providing analysis for nucleic acids. Composition, codon usage and repeat motifs may all be established using this portion of the software. Other analyses such as restriction mapping, primer design, translation and mutation may also be performed.

Protein analysis is a further feature within the EMBOSS suite of bioinformatics applications. There are 41 protein analysis programmes currently available for analysis of amino acid sequences including secondary structure prediction, pattern recogniton and composition analysis.

12 separate utilites to create and index databases are also modules within the EMBOSS suite, enabling you to build and query your own sequence repositories.

Futher programs contribute to the general analysis content of the suite, offering simulation opportunities such as Michaelis-Menten kinetics, or the creation of phylogenetic distance matrices.

The beauty of the EMBOSS system is its unlimited capacity for sequence data - there are no arbitrary constraints. In the post-genomic era, it offers a valuable tool for the analysis of much larger data sets. EMBOSS does not have its own data format, but will read and write 42 different sequence and structure formats used by other software applications.

The full distribution, including all applications, their documentation, relevant databases and the Jemboss interface will occupy approximately 145 Mb disk space. The Cygwin addition for Windows requires approximately 1.6 Gb. It is recommended that your computer has a RAM capacity of at least 256 Mb, although the programmes will function with 128 Mb RAM.

For those with some scripting or coding skills, individual applications may be inserted into existing or newly created scripts to enable customised analysis of your data. Scripts may also call library functions, allowing you to create your own applications for specific use within your workplace.

Utilities are written in the EMBOSS programmming language, coded in C and borrowing concepts from C++. This language involves function calls from two different libraries, NUCLEUS and AJAX. The former library holds functions specific to sequence analysis, including sequence comparisons, translation, codon usage and annotation, whilst AJAX covers standard data structures, including strings, sequences, filehandles, queues, hashes, heaps, lists, dictionaries, trees and dynamic arrays. It also covers standard algorithms including comparisons, pattern matching, sorting, and iterators.