Sequence Retrieval System features

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). 

As shown in Fig. 1.1, bioinformatics approaches in pharmacogenomics are conducted systematically. The lowest level in the system is at the molecular level. At this level, it is necessary to understand the detailed features of a gene and the relationship between genetic structure and function (see Subheading 1.2.1). These detailed features include sequence analytic information such as sequence retrieval and comparison, sequence variation information such as about single-nucleotide polymorphisms (SNPs), and sequence patterns that can correlate sequence structure to functional motifs. 

The amino acid sequences can be searched and retrieved from the integrated retrieval sites such as Entrez (Schuler et al., 1996), SRS of EBI (http //srs.ebi.ac.uk/), and DDBJ (http //srs.ddbj.nig.ac.jp/index-e.html). From the Entrez home page (http //www.ncbi.nlm.nih.gov/Entrez), select Protein to open the protein search page. Follow the same procedure described for the Nucleotide sequence (Chapter 9) to retrieve amino acid sequences of proteins in two formats GenPept and fasta. The GenPept format is similar to the GenBank format with annotated information, reference(s), and features. The amino acid sequences of the EBI are derived from the SWISS-PROT database. The retrieval system of the DDBJ consists of PIR, SWISS-PROT, and DAD, which returns sequences in the GenPept format. 

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