Information retrieval from biological databases.

As discussed earlier in this book, GenBank was created in response to the explosion in sequence information resulting from a panoply of scientific efforts such as the Human Genome Project. To review, GenBank is an annotated collection of all publicly available DNA and protein sequences and is maintained by the National Center for Biotechnology Information (NCBI). As of this writing, GenBank contains 7 million sequence records covering almost 9 billion nucleotide bases. Sequences find their way into GenBank in several ways, most often by direct submission by individual investigators through tools such as Sequin or through ‘‘direct deposit’’ by large genome sequencing centers. GenBank, or any other biological database for that matter, serves little purpose unless the database can be easily searched and entries retrieved in a usable, meaningful format. Otherwise, sequencing efforts have no useful end, since the biological community as a whole cannot make use of the information hidden within these millions of bases and amino acids. Much effort has gone into making such data accessible to the average user, and the programs and interfaces resulting from these efforts are the focus of this chapter. The discussion centers on querying the NCBI databases because these more ‘‘general’’ repositories are far and away the ones most often accessed by biologists, but attention is also given to a number of smaller, specialized databases that provide information not necessarily found in GenBank.