Table 2 Database feature comparison
From: A comparative proteomics resource: proteins of Arabidopsis thaliana
Databases | Features | Scope | Level of integration | Learning curve | Drawbacks |
|---|---|---|---|---|---|
Entrez Genome [20] | Domains from CDD (SMART, PFAM) Proteins by NCBI GI number, accession number, Swiss Prot ID, and so on Structure by PDB ID 3D domains from MMDB Domain relatives by CDART Related sequences using BLINK Visualization using Cn3D Public data | All sequences published or voluntarily deposited 1,000+ genomes | High | Easy to high | Complex system Only experimental structural information is available Software interface is not readily available Linkout progress is slow |
EBI Proteome Analysis Database [43] | InterPro member databases (SwissProt, PFAM, SMART, TIGRFAM, PRINTS, PROSITE, ProDom, PIR SuperFamily) Families, domains and sites by member databases GO annotation Manual curation and integration Precomputed matches against InterPro entries | Complete proteomes in SwissProt and TrEMBL 110+ proteomes | Medium | Easy to moderate | SRS based query interface free to academia Basic keyword search possible Sequence based classification |
MatDB | Arabidopsis annotation from PEDANT Free text search Protein categories by structure, function based on SCOP, PIR, InterPro | Arabidopsis with limited intergenome comparison | Medium | Easy to moderate | Query response time varies SCOP classification mildly difficult to use |
Proteins of Arabidopsis thaliana (PAT) database | Domains from SCOP, predicted domains from PDP, and full length PDB chains with less than 90% sequence identity (FOLDLIB) GO annotation Precomputed matches against FOLDLIB Template-based structure models Visualization using QuickPDB, Chime Advanced keyword search Hierarchical browsing based on SCOP Related sequences using WU-BLAST | Currently 87 Expanding to provide coverage for all known proteomes | Medium | Easy to Moderate | Presentation Style Query flexibility implies a higher learning curve |
TAIR | GO and other ontology development Sequence and map viewer Domains from InterPro Regulatory motif analysis User annotation | Comprehensive resource devoted to Arabidopsis | Medium | Easy to moderate | No structural information |
SUPERFAMILY | HMM (SAM) models for SCOP domains Fold recognition Domain architecture visualization | 107 genomes | Low to medium | Easy to moderate | Presentation style No update information |
Gene 3D | Structural assignment based on CATH domain classification using PSI-BLAST | 66 genomes | Low | Easy | Annotation not dynamically linked to CATH No update information |