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