GenBank records

SeqHound is the basis for many of Blueprint s applications. The BIND Interaction Viewer 3.0 queries SeqHound to recover sequence annotation and interaction information. SeqHound has been used as a back end to replace all previous calls to the NCBI for retrieval of data such as GenBank records, taxonomy traversal, DNA and protein sequence by taxonomy ID or organism, 3D neighbors, and GO traversal. Recently the SeqHound API has been incorporated into Tavema [15], which allows biologists to assemble Web services into a pipeline. The current Web interface allows access only to the sequence aspects of the database, as the primary aim of SeqHound was to be a resource for programmers. However, a more fully featured interface is under development, which will make most of the API s functionality available to nonprogrammers. 

This modified PASTA file now has the gi number (see below and Chapter 2), the GenBank accession number, the LOCUS name, and the DEPINITION line from the GenBank record. The record was passed from the underlying ASN.l record (see Appendix 3.2), which NCBI uses to actually store and maintain all its data. 

Each GenBank record must have at least one reference or citation. It offers scientihc credit and sets a context explaining why this particular sequence was determined. In many cases, the record will have two or more reference blocks, as shown in Appendix 3.1. The preceding sample indicates a published paper. There is a MEDLINE and PubMed identifier present that provides a link to the MEDLINE/ PubMed databases (see Chapter 7). Other references may be annotated as unpublished (which could be submitted) or as placeholders for a publication, as shown. 

The last citation is present on most GenBank records and gives scientific credit to the people responsible for the work smroimding the submitted sequence. It usually includes the postal address of the first author or the lab where the work was done. The date represents the date the record was submitted to the database but not the date on which the data were first made public, which is the date on the locus line if the record was not updated. Additional submitter blocks may be added to the record each time the sequences are updated. 

The Source Feature. The source feature is the only feature that must be present on all GenBank records. All features have a series of legal qualifiers, some of which are mandatory (e.g., /organism for source). All DNA sequence records have some origin, even if synthetic in the extreme case. In most cases, there will be a single source feature, and it will contain the /organism. Flere is what we have in the example from Appendix 3.1 ... 

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