EMBOSS User's Guide

Peter Rice is a group leader at the European Bioinformatics Institute (EBI, Hinxton, UK), a centre for research and services in bioinformatics and part of the European Molecular Biology Laboratory (EMBL). His group investigates and advises on the e-Science and Grid technology requirements of the EMBL-EBI, through application development plus participation in standards development. His group also houses the EMBOSS project. Dr Rice instigated EMBOSS in 1996 when he was based at the Sanger Centre (Hinxton, UK), with Alan Bleasby (SEQNET, Daresbury) and in collaboration with Thure Etzold (EMBL-EBI). He left Sanger in 2000 to work for LION Biosciences, and in 2003 joined the EMBL-EBI. Alan Bleasby is a Senior Scientific Officer at EMBL-EBI. He developed the early EMBOSS programming library (AJAX) at Daresbury Laboratory (Warrington, UK) where he was responsible for the SEQNET UK national bioinformatics service. Dr Bleasby moved to the UK Medical Research Council Human Genome Mapping Project Resource Centre (UK HGMP-RC) when the SEQNET and HGMP-RC services merged in early 1999, where he was Group Leader of the Proteomics Applications Group and coordinated EMBOSS. When the HGMP-RC closed in 2005, he moved to the EBI to work full-time on EMBOSS. Jon Ison is a Senior Scientific Officer at EMBL-EBI. He moved from Leeds to the UK HGMP-RC in 1999 to work on the Collaborative Computing Project in Biosequence and Structure Analysis (CCP11), before taking the post of Software Specialist for the Proteomics Applications Group in 2000. Dr Ison has been a lead contributor and developer of EMBOSS since then, moving in 2005 with Alan Bleasby to the EMBL-EBI where he helps coordinate the project with Peter Rice and Alan Bleasby.

Acknowledgements; 1. Preface; 2. Conventions used in the manual; 3. Welcome to the EMBOSS user's manual; 4. Background to EMBOSS; 5. Basic set-up and maintenance; 6. Getting started; 7. Tutorial; 8. File formats; 9. The EMBOSS command line; 10. Applications and packages; 11. EMBOSS application reference; 12. EMBASSY application reference; 13. Interfaces; 14. Using EMBOSS under wEMBOSS; 15. Using EMBOSS under Jemboss.