Submissions Sequin

Many journals require submission of sequence information to a database prior to publication so that an accession number may appear in the paper. NCBI has a WWW form, called Banklt. for convenient and quick submission of sequence data. Sequin. NCBI s stand-alone submission software for MAC, PC, and IINIX nlatfnrmg k ako available hvFTP When lining Sennln... 

The Local sequence identifier is most prominently used in the data submission tool Sequin (see Chapter 4). Each sequence will eventually get an accession, version identifier and a gi number, but only when the completed submission has been processed by one of the public databases. During the submission process, Sequin assigns a local identifier to each sequence. Because many of the software tools made by NCBl require a sequence identifier, having a local Seq-id allows the use of these tools without having to first submit data to a public database. 

The Nuc-prot set, containing a nucleotide and one or more protein products, is the type of set most frequently produced by a Sequin data submission. The component Bioseqs are coimected by coding sequence region (CDS) features that describe how translation from nucleotide to protein sequence is to proceed. In a traditional nucleotide or protein sequence database, these records might have cross-references to each... 

The World Wide Web is now the most common interface used to submit sequences to the three databases. The Web-based submission systems include Sakura ( cherry blossoms ) at DDBJ, Webln at EBI, and Bankit at the NCBI. The Web is the preferred submission path for simple submissions or for those that do not require complicated armotations or too much repetition (i.e., 30 similar sequences, as typically found in a population study, would best be done with Sequin, see below). The Web form is ideal for a research group that makes few sequence submissions and needs something simple, entailing a short learning curve. The Web forms are more than adequate for the majority of the submissions some 75-80% of individual submissions to NCBI are done via the Web. The alternative addresses (or URLs) for submitting to the three databases are presented in the list at the end of the chapter. 

Sequin begins with a window that allows the user to start a new submission or load a file containing a saved record. After the iiutial submission has been built, the record can be saved to a file and edited later, before finally being sent to the database. If Sequin has been configured to be network aware, this window also allows the downloading of existing database records that are to be updated. 

The sequence editor built into Sequin automatically adjusts feature intervals as the sequence is edited. This is particularly important if one is extending an existing record by adding new 5 sequence. Prior to Sequin, this process entailed manually correcting the intervals on all biological features on the sequence or, more likely, redoing the entire submission from scratch. The sequence editor is used much like a text editor, with new sequence being pasted in or typed in at the position of a cursor. 

A finished submission can be saved to disk and E-mailed to one of the databases. It is also a good practice to save frequently throughout the Sequin session, to make sure nothing is inadvertently lost. The list at the end of this chapter provides E-mail addresses and contact information for the three databases. 

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