The document provides an overview of the Universal Protein Resource Knowledgebase (UniProtKB), detailing its two main components, Swiss-Prot and TrEMBL, which contain manually annotated and computationally annotated protein information, respectively. It emphasizes the high level of annotation, minimal redundancy, and integration with other databases, while also presenting statistics regarding the number of entries. Additionally, it discusses the continuous enhancement of Swiss-Prot's format and content to support proteomics and the use of automated procedures while maintaining annotation quality.

1. Swiss – Prot
SAGRIKA CHUGH
(M.Tech Bioinformatics)
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2. INTRODUCTION
• The Universal Protein Resource Knowledgebase (UniProtKB) is the central hub for the
collection of functional information on proteins.
It consists of two sections:
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Swiss -Prot
• Reviewed
• Manually annotated
• Records with information extracted from
literature and curator-evaluated
computational analysis.
Tr-EMBL (Transalted European
Molecular Biological Labratory)
• Unreviewed
• Computationally annotated
• Records that await full manual
annotation.

3. Source: http://www.uniprot.org/
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4. • Created at the Department of Medical Biochemistry of the University of Geneva and
works in collaboration with the European Molecular Biology Laboratory (EMBL), since
1987
• Swiss-Prot strives to provide high level of annotation , minimal level of redundancy
and integration with other databases
• It is now an equal partnership between the EMBL and the Swiss Institute of
Bioinformatics (SIB)
• TrEMBL, a computer-annotated supplement to Swiss-Prot.
• Similar format to European Bioinformatics Institute Nucleotide Sequence Database
(EMBL)
INTRODUCTION
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5. Features of Swiss-Prot
• Annotation
• Minimal Redundancy
• Integration with other databases
• Documentation
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6. Annotation
Data
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Core data Annotation
• sequence data
• the citation information (bibliographical
references)
• taxonomic data (description of the
biological source of the protein)
• Post-translational modification(s). for
example phosphorylation, acetylation, etc.
• Domains and sites. for example calcium
binding regions, zinc fingers.
• Secondary structure. For example alpha
helix, beta sheet, etc.
• Quaternary structure. For example
homodimer, heterotrimer, etc.
• Disease(s) associated with deficiencies in
the protein

7. Minimal redundancy
• Much of data comes from more than one literature report
• Data condensed and merged to appear more concise and coherent
• Conflicts in data are listed for each entry
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8. Integration with other databases
• Swiss-Prot provides cross-references to external data collections
• Integration between the three types of sequence-related databases (nucleic acid
sequences, protein sequences and protein tertiary structures)
• Swiss-Prot Sample Entry swiss prot entry.txt
• Original entry Aar2 - Protein AAR2 homolog - Mus musculus (Mouse) - Aar2 gene & protein.html
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9. Documentation
• All files documented and indexed.
• Documentation kept up-to-date.
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10. Swiss-Prot Statistics
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Number of entries
New entries 245
Updated entries 64,182
Unchanged entries 489,047
Total 553,474
Entries with updated sequences 40
With a fragmented AA sequence 9,143
With known alternative products 24,759
Source http://www.uniprot.org/statistics/Swiss-Prot
(Jan 18, 2017 release)

11. TrEMBL: A computer-annotated supplement to Swiss-PROT
• TrEMBL (translation of EMBL nucleotide sequence database) in 1996..
Why TrEMBL ?
• Increased data flow from genome projects to the sequence databases.
• To maintain the high annotation quality.
• To make sequences available as quickly as possible..
• TrEMBL consists of computer-annotated entries derived from the translation of all
coding sequences (CDS) in the nucleotide sequence databases, except for CDS
already included in Swiss-PROT.
• It also contains protein sequences extracted from the literature and protein sequences
submitted directly by the user community.
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12. TrEMBL
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Sp- TrEMBL
(SWISS PROT-TrEMBL)
REM-TrEMBL
(Remaining TrEMBL)
contains sequences, which will eventually
be incorporated into SWISS-PROT
contains those sequences which will not be
incorporated into SWISS-PROT.
For eg synthetic sequences, patent
application sequences, fragments of less
than 8 amino acids and coding sequences
where there is strong experimental
evidence that the sequence does not code
for a real protein.

13. Tr-EMBL Statistics
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Number of entries
New entries 3,031,100
Updated entries 20,906,527
Unchanged entries 49,774,254
Total 73,711,881
Entries with updated sequences 746
With a fragmented AA sequence 8,492,670
With known alternative products 0
Source:http://www.uniprot.org/statistics/TrEMBL
Jan 18, 2017 release

14. Summary
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Source: www.expasy.org

15. CONCLUSION
• Swiss-Prot continuously enhanced its format and content to adjust to the wide
knowledge pool in proteomics along with high quality of annotation.
• Automated annotation procedures are used for Swiss-Prot in a very conservative
manner.
• The extensive integration of SWISS-PROT with specialized databases enables users
to navigate through the current knowledge in the Life Sciences providing an insight into
the universe of proteins.
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16. References
• The Swiss-PROT protein knowledgebase and its supplement TrEMBL in
2003 Brigitte Boeckmann etal Nucl Acids Res (2003) 31 (1): 365-370.
• The Swiss-PROT protein sequence database and its supplement TrEMBL in
2000 Amos Bairoch, Rolf Apweiler Nucl Acids Res (2000) 28 (1): 45-48.
• The Swiss-PROT protein sequence data bank and its supplement TrEMBL in
1999 Amos Bairoch ,Rolf Apweiler Nucl Acids Res (1999) 27 (1): 49-54
• The Swiss-PROT protein sequence data bank and its supplement TrEMBL Amos
Bairoch Rolf Apweiler Nucl Acids Res (1997) 25 (1): 31-36.
• The Swiss-PROT Protein Sequence Data Bank and Its New Supplement
TREMBL Amos Bairoch Rolf Apweiler Nucl Acids Res (1996) 24 (1): 21-25.
• http://www.uniprot.org/uniprot/
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