Swiss prot

The Universal Protein Resource Knowledgebase (UniProtKB) is the central hub for the collection of functional information on proteins.

1. SWISS PROT PRESENTED BY: Dr. Shikha Thakur

2. SWISSPROT INTRODUCTION The universal Protein Resource knowledgebase ( UniProtKB ) is the central hub for the collection of functional information on proteins.

3. It consists of two sections: Swiss- Prot Tr -EMBL (Translated European Molecular Biological Laboratory) Reviewed Unreviewed Manually annotated Computationally annotated Records with information extracted from literature and curtor -evaluated computational analysis. Records that await full manual annotation.

4. Introduction 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 Data (EMBL).

5. Features of Swiss- Prot Annotation Minimal Redundancy Integration with other databases Documentation

6. Annotation Data Core Data Annotation Sequence data Post-translational modifications for example phosphorylation, acetylation etc. The citation information (bibliographical references) Domains and sites. For example calcium binding regions , zinc fingers. Taxonomic data (description of the biological source of the protein). Secondary structure. For example alpha helix, beta sheet, etc. Quaternary structure. For example homodimer, heterodimer, etc. Diseases 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.

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.

9. Documentation All files documented and indexed. Documentation kept up-to-date.

10. TrEMBL : A computer-annotated supplement to Swiss-PROT TrEMBL (translation of EMBL nucleotide sequence database) in 1996.. Why TrEMBL ? Increase 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.

11. TrEMBL 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 synthethic 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.

12. 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 datbases enables users to navigate through the current knowledge in the life Siences providing an insight into the universe of proteins. Swiss- Prot continoiusly enhanced its format and content to adjust to the wide knowledge pool in proteomics along with high quality of annotation.

13. 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.