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Questions and Answers
What is the primary goal of merging data from various sources in SWISS-PROT?
What is the primary goal of merging data from various sources in SWISS-PROT?
Which of these is NOT a criterion used by SWISS-PROT to distinguish itself from other protein sequence databases?
Which of these is NOT a criterion used by SWISS-PROT to distinguish itself from other protein sequence databases?
Which of the following is considered core data in SWISS-PROT?
Which of the following is considered core data in SWISS-PROT?
What are the three main categories of information found in SWISS-PROT annotation?
What are the three main categories of information found in SWISS-PROT annotation?
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What is the primary function of the Protein Information Resource (PIR)?
What is the primary function of the Protein Information Resource (PIR)?
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Which of the following databases is NOT included in the PIR-NREF database?
Which of the following databases is NOT included in the PIR-NREF database?
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What is the main purpose of the superfamily classification in PIR-PSD?
What is the main purpose of the superfamily classification in PIR-PSD?
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Which of the following is NOT a feature of the Martinsried Institute for Protein Sequence (MIPS) database?
Which of the following is NOT a feature of the Martinsried Institute for Protein Sequence (MIPS) database?
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What is the purpose of the TREMBL database?
What is the purpose of the TREMBL database?
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SWISS-PROT always includes complete source code for all proteins in the database.
SWISS-PROT always includes complete source code for all proteins in the database.
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The superfamily classification in PIR-PSD is based on the assumption that protein families are non-overlapping.
The superfamily classification in PIR-PSD is based on the assumption that protein families are non-overlapping.
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MIPS primarily focuses on collecting and annotating protein sequences from yeast organisms.
MIPS primarily focuses on collecting and annotating protein sequences from yeast organisms.
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One of the key goals of PIR-NREF is to minimize redundancy in protein sequence data by integrating sequences from multiple databases.
One of the key goals of PIR-NREF is to minimize redundancy in protein sequence data by integrating sequences from multiple databases.
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The TREMBL database is intended to be a complete and comprehensive source of protein sequences, including all known variants and isoforms.
The TREMBL database is intended to be a complete and comprehensive source of protein sequences, including all known variants and isoforms.
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What is the main reason for the inclusion of TREMBL in SWISS-PROT releases?
What is the main reason for the inclusion of TREMBL in SWISS-PROT releases?
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Study Notes
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.
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