Sequence Retrieval System

In the bioinformatics realm, SRS (Sequence Retrieval System) [2] is a popular system, which uses a centralized collection of data resources primarily in flat text file form and, more recently, handles XML (Extensible Markup Language) files as well. Data resources are treated in a federated manner since each is maintained in its original form. However, SRS contains a large number of cross-references between corresponding fields in various data sources, so that keyword searches can be done across them. SRS thus performs more structured searches across the information than what a simple text search provides (such as web indexes perform, for example). Even though the data model implicit in the cross-reference tables is not very deep, SRS provides a useful way for users to browse and do simple queries across a large number of data sources as well as to integrate results from some computational methods. 

Searches for similar protein and nucleic acid sequences Protein structures on moving 3D coordinates Sequence retrieval system for cross-referencing databases Searches for similar protein sequences Database of gene sequences... 

BLAST Chime Entrez (NCBI) FASTA GenBank (NCBI) Molecules R Us RasMol (Ras Mac) SRS (EMBL) Searches for similar protein and nucleic acid sequences Protein structures on moving 3D coordinates Sequence retrieval system for cross-referencing databases Searches for similar protein sequences Database of gene sequences Provides coordinates for protein 3D structure and manipulation Provides coordinates for protein 3D structure and manipulation Sequence retrieval system for cross referencing databases... 

The Sequence Retrieval System (Etzold et ah, 1996) is a network browser for databases at EBI. The system allows users to retrieve, link, and access entries from all the interconnected resources such as nucleic acid, EST, protein sequence, protein pattern, protein structure, specialist/boutique, and/or bibliographic databases. The SRS is also a database browser of DDBJ, ExPASy, and a number of servers as the query system. The SRS can be accessed from EBI Tools server at http // www2.ebi.ac.uk/Tools/index.html or directly at http //srs6.ebi.ac.uk/. The SRS permits users to formulate queries across a range of different database types via a single interface in three different methods (Figure 3.4) ... 

Figure 3.4. Query form for Sequence Retrieval System (SRS).

The European Bioinformatics Institute (EBI). This site is located at Hinxton Hall, Cambridge, UK. The home of the EMBL Nucleotide Sequence Database data management tools [including publicly accessible version of SRS—the Sequence Retrieval System (7)] protein family databases microarray tools etc. An extensive repository of resources for bioinformatics. 

The Sequence Retrieval System (SRS [19]), initially developed at EMBL and the European Bioinformatics Institute, uses an interesting approach by combining the features of data warehouses and federated database systems. SRS is on the one hand heavily indexing locally stored genomic flat file databases and, on the other hand, it allows one to query DBMS on different sites. An example for a federated approach is the Mouse Federated Database of the Comparative Mouse Genomics Centers Consortium (http //www.niehs.nih. gov/cmgcc/dbmouse.htm). 

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