Chapter 4. Databases

Table of Contents

4.1. General Database Configuration
4.1.1. Sequence Database Support
4.1.1.1. Query Levels, Access Methods and Attributes
4.1.2. Configuring EMBOSS to work with Databases
4.1.3. Example Database Definition File (emboss.default.template)
4.1.4. Test Databases
4.1.5. Testing your Database Definitions
4.2. Database Attributes
4.2.1. Introduction
4.2.2. Description of Attributes
4.2.2.1. method, methodall, methodentry, methodquery
4.2.2.2. format, formatentry, formatquery, formatall
4.2.2.3. type
4.2.2.4. fields
4.2.2.5. directory
4.2.2.6. filename
4.2.2.7. exclude
4.2.2.8. indexdirectory
4.2.2.9. url
4.2.2.10. proxy
4.2.2.11. httpversion
4.2.2.12. app, appentry, appquery, appall
4.2.2.13. dbalias
4.2.2.14. comment
4.2.2.15. release
4.2.2.16. hasaccession
4.2.2.17. caseidmatch
4.3. Database Access Methods
4.3.1. Introduction
4.3.2. Description of Database Access Methods
4.3.2.1. EMBOSS
4.3.2.2. EMBLCD
4.3.2.3. SRS
4.3.2.4. SRSFASTA
4.3.2.5. SRSWWW
4.3.2.6. BLAST
4.3.2.7. EMBOSSGCG
4.3.2.8. GCG
4.3.2.9. DIRECT
4.3.2.10. URL
4.3.2.11. APP
4.3.3. Mixed Access Methods
4.3.4. Database Farms
4.4. Miscellaneous Database Integration
4.4.1. REBASE
4.4.2. TRANSFAC
4.4.3. PROSITE
4.4.4. PRINTS
4.4.5. AAINDEX
4.4.6. CUTG
4.4.7. JASPAR
4.4.8. Miscellaneous Data Files
4.5. Database Indexing
4.5.1. Introduction
4.5.2. Resource Definitions, Cachesize and Pagesize
4.5.3. Indexing and Configuration
4.5.3.1. Flatfile Databases
4.5.3.2. GCG Format Databases
4.5.3.3. BLAST Databases
4.5.3.4. FASTA Databases
4.5.3.5. Other Databases
4.5.4. Configuring EMBOSS to use SRS for Database Look-up
4.5.5. Size of the dbx* Indexes