GenPept format

Figure 4.7. GenPept format for amino acid sequence of chicken egg-white lysozyme.

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. 

PIR (upper), Swiss-Prot (middle) and GenPept (lower) formats for amino acid sequence of chicken egg-white lysozyme are represented. Swiss-Prot format is the default format of EMBL/EBI and GenPept format is the default format adopted by GenBank (Entrez) and DDBJ (DBGet). Pasta format is shown in subsection 5.1.2. 

The annotated amino acid sequence files normally provide information concerning the sites and types for post-translational modifications and functions. These descriptions can be found from Features line(s) in all of the three sequence formats, namely, PIR, GenPept, and Swiss-Prot. The ExPASy Proteomics tools (http //www.expasy. ch/tools/) provide numerous links for such services. 

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