Table 3 Processing time statistics of some utilities in BDE
From: BioDB extractor: customized data extraction system for commonly used bioinformatics databases
Database | Type of input data: (Number of IDs) | Size of data being parsed (Mb) | Utility | Time (seconds)a |
|---|---|---|---|---|
EMBL-ENA | Genes: 250 | 12.4 | Basic Fields Search (All Fields are selected) | 80 |
Advanced Feature Table Search | 95 | |||
Genomes: 100 (Viral & bacterial) | 137 | Basic Fields Search (All Fields are selected) | 120 | |
UniprotKB | Proteins: 250 | 2 | Advanced Feature Table Search | 30 |
Proteins: 250 | 2 | Topic-wise Comments Extractor | 30 | |
PDB | Structures: 250 | 200 | Chain_Finder & Seq_Extractor | 120 |
Structures: 250 | 200 | PDB to GO Mapping | 100 | |
KEGG | Organisms: 10 | - | Customized searches for Pathway data (GENE) | 45 |
DrugBank | Drugs: 250 | 14 | Basic Fields Search (All Fields are selected) | 70 |