4. Chapter 4. Databases

EMBOSS supports all the common data formats you are likely to need. This chapter gives comprehensive information on the configuration of databases and miscellaneous data files for use with EMBOSS. It explains the syntax used to write database definitions in the EMBOSS system file (emboss.default), including possible attributes and access methods. Ways to test your database definitions and the test databases included in EMBOSS are described. The indexing and configuring of flatfile, GCG format, BLAST, FASTA and other databases is covered, including ways to fine tune a database installation and configure EMBOSS to use SRS for database look-up.