2 - Nucleic Acid and Protein Sequence Databases

Abstract

This chapter describes nucleic acid and protein sequence databases. The most common uses of the sequence databases are to search for similarity with an unknown query sequence and to search for entries matching keywords in their annotation. There are two main nucleic acid sequence databases and one main protein sequence database in widespread general use amongst the biological community. The exchange of sequences occurs daily, so that each of the three main databases holds the same data. The sequence data is exactly the same in each database. It is common for database searching systems such as the Entrez or BLAST WWW sites to merge different databases into one nonredundant database. Submissions to any of the three nucleic acid databases are forwarded daily for inclusion in the other two. The sequences can normally only be altered by the authors. The EMBL, GenBank, and DDBJ databases share a common feature table format. It is found that the purpose of the feature table is to show information on biologically meaningful features in the sequence entry and to indicate variants of the sequence.