Untitled Quiz

SWISS-PROT Database

• SWISS-PROT is a protein sequence database, established in 1986, and maintained by the Department of Medical Biochemistry at the University of Geneva and the EMBL Data Library.
• The database contains sequence entries comprised of different line types with unique formats.
• It follows the EMBL nucleotide sequence database format closely for standardization.
• SWISS-PROT is distinguished from other databases by its annotation, minimal redundancy, and integration with other databases.

Annotation

• SWISS-PROT data includes core data (sequence information, citations, taxonomic data) and annotation.
• Annotation details include protein function, post-translational modifications (e.g., carbohydrates, phosphorylation), domains and sites (e.g., calcium binding, ATP binding), secondary/tertiary structure, protein similarities, diseases associated with deficiency, sequence conflicts, and variants.
• Annotation is mainly located in comment lines (CC), feature tables (FT), and keyword lines (KW). Comments are categorized by "topics" for efficient data retrieval.

Minimal Redundancy

• SWISS-PROT aims to minimize redundancy by merging sequencing reports and indicating conflicts in the feature table of the corresponding entry.

Integration with Other Databases

• SWISS-PROT is cross-referenced with 24 different databases to provide links to related information.
• The databases referenced often contain literature, nucleic acid sequences, protein sequences, protein tertiary structures, and specialized data collections.
• The selected organisms for annotation include Arabidopsis thaliana, Bacillus subtilis, Drosophila melanogaster and more.

PIR (Protein Information Resource)

• PIR is a resource for protein sequence identification and interpretation.
• It was established in 1984, and since 1988, maintained by PIR-International.
• This association includes the Protein Information Resources at NBRF, the international protein information database of Japan (JIPID), and the Martinsried Institute for Protein Sequences (MIPS).

PIR-PSD (Protein Sequence Database)

• PIR-PSD is an annotated protein database with over 283,000 sequences covering the entire taxonomic range.
• It focuses on superfamily classification, superfamily curation (signature domains, member categorization), and bibliography mapping and attribution.
• This enables automated classification of sequences and permits creating alignments and phylogenetic trees.

PIR-NREF (Non-redundant REFerence) Database

• PIR-NREF collects protein sequences from PIR-PSD, SWISS-PROT, TrEMBL, RefSeq, GenPept, and PDB, totaling over a million entries.
• It includes identical sequences, identical subsequences, and highly similar sequences (>95% identity) from multiple sources.
• PIR-NREF aids in protein identification and sequence searching across the entire sequence collection or portions of specific genomes.

TREMBL (TRanslation from EMBL)

• The TREMBL database is a supplement to SWISS-PROT, containing translations of coding sequences from the EMBL nucleotide sequence database that haven't been incorporated yet to maintain SWISS-PROT's quality.
• TREMBL is split into SP-TREMBL and REM-TREMBL.
• SP-TREMBL is merged with known SWISS-PROT entries for minimal redundancy.
• REM-TREMBL contains unmerged entries, including sections on immunoglobulins, T-cell receptors, and synthetic/incomplete sequences.