GenBank submitting sequence data

Biological raw data are stored in public databanks (such as Genbank or EMBL for primary DNA sequences). The data can be submitted and accessed via the World Wide Web. Protein sequence databanks like trEMBL provide the most likely translation of all coding sequences in the EMBL databank. Sequence data are prominent, but also other data are stored, e.g.yeast two-hybrid screens, expression arrays, systematic gene-knock-out experiments, and metabolic pathways. 

Various verification steps have been introduced to ensure that SPTR is comprehensive and contains all relevant data sources. The main source of new protein sequences is the translations of CDS in the nucleotide sequence databases. The up-to-date inclusion of new protein sequence entries is ensured by the weekly translation of EMBL-NEW (the updates to the EMBL nucleotide sequence database). The three collaborating nucleotide sequence databases DDBJ, EMBL, and GenBank exchange their data on a daily basis. Therefore any protein coding sequence submitted to DDBJ/EMBL/GenBank will appear in SPTR within 2 weeks in the worst case and within less than 1 week in the average case. 

Although this chapter is about the GenBank nucleotide database, GenBank is just one member of a community of databases that includes three important protein databases SWISS-PROT, the Protein Information Resomce (PIR), and the Protein DataBank (PDB). PDB, the database of nucleic acid and protein structures, is described in Chapter 5. SWISS-PROT and PIR can be considered secondary databases, curated databases that add value to what is already present in the primary databases. Both SWISS-PROT and PIR take the majority of their protein sequences from nucleotide databases. A small proportion of SWISS-PROT sequence data is submitted directly or enters through a journal-scanning effort, in which the sequence is (quite literally) taken directly from the published literature. This process, for both SWISS-PROT and PIR, has been described in detail elsewhere (Bairoch and Apweiller, 2000 Barker et al., 2000.)... 

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 UniProt Archive (UniParc) provides a stable, comprehensive, nonredundant sequence collection by storing the complete body of publicly available protein sequence data. Although most protein sequence data are derived from the translation of DDBJ/EMBL/GenBank sequences, primary protein sequence data are also submitted directly to UniProt or derived from the PDB entries. The Archive also captures protein sequence data from other sources such as Ensemble, International Protein Index (IPI), NCBI-RefSeq, FlyBase, and WormBase. Each protein sequence is assigned to a unique UniParc identifier (UPI ) and represented only once in the Archive. In UniParc, the... 

There are four textboxes with corresponding data field selectors. After entering querystrings to textboxes and choosing data fields, select sequence formats (embl, fasta or genbank) and then click the Submit Query button to begin the search. 

If it is necessary to upload sequence files, these can be compressed using either WinZip, or the UNIX gzip utility, which will significantly reduce the time taken to upload the data. Submitted files should each contain a single sequence in EMBL or FASTA format. It is preferable to use EMBL/Genbank format for uploaded sequences, because any genes annotated in the feature table will then be displayed by ACT. Should multiple sequences be present in an uploaded file, only the first will be used. 

Standard query Select the databanks and click Standard button under Query forms. This opens the standard query form where the user is given choices of data fields to search, operator to use, wild card to append, entry type and result views. There are four textboxes with corresponding data field selectors. After entering query strings to textboxes and choosing data fields, select sequence formats (embl, fasta or genbank) then click the Submit Query button to begin the search. 

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