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Sequin Network Aware SequinMost features of Sequin are identical whether the program is used in its stand-alone or network-aware mode. However, the network-aware mode allows users to perform some additional tasks. You can easily determine whether Sequin is in its stand-alone or network aware mode by looking at the first screen, entitled "Welcome to Sequin." If you see a button called "Download from Entrez," you are running Sequin in its network aware mode. Instructions on how to make Sequin network-aware are provided in the Sequin help documentation. Updating existing GenBank records Using Sequin in its network-aware mode, users can download an existing GenBank record from Entrez using the GenBank accession number or GI identification number (NID). Once this record is open in Sequin, its sequence can be updatated in the Sequence Editor, or its annotations modified in the appropriate forms. The record can then be resubmitted to GenBank as a sequence update. Please note that, at present, you can update only those
records which you have previously submitted yourself.
When you download the record from Entrez, Sequin will
ask you if you are submiting it as an update. If you
answer "yes," you will be prompted to enter the contact
information, as if you were preparing a new submission.
Performing a PowerBLAST search PowerBLAST is a new version of the BLAST application which displays sequence comparison results in a graphical format. In its network-aware mode, Sequin can perform a PowerBLAST search of your sequence against the nucleotide and protein databases at the NCBI. You can use the results of these comparisons for annotation purposes. Screening for vector and mitochondrial DNA Sequences submitted to GenBank are always screened for the presence of contaminating vector or mitochondrial DNA. The database staff then remove any such sequences from the record. The network-aware mode of Sequin allows you to screen your nucleotide sequence for any unwanted contaminants, and remove the vector and mitochondrial sequences before you submit the record. Performing a Medline lookup In its network-aware mode, Sequin contains a built-in function that will look up the title, authors, and journal sections of a Medline record if certain minimal information provided. Thus, users who add information about publications pertaining to the sequence do not need to enter the entire citation manually. Sequin can find articles based on their Medline Unique Identifier (MUID), or Journal name, date, volume, and pages. Users should be aware that there often a delay between the time when a journal article appears in press and the time when it is issued a MUID. Without a MUID, the Medline lookup cannot be performed. Performing a Taxonomy lookup A taxonomy lookup is performed by the NCBI database staff after the record has been submitted to GenBank. Using Sequin in its network-aware mode, interested users can themselves look up the taxonomic lineage of the organism from which the sequence is derived. Taxonomy lookups are performed through the NCBI's taxonomy database. If the taxonomy lookup fails for the organism from which your sequence is derived, please consult the taxonomy WWW page. If your organism is not listed, or if you disagree with the lineage we have specified, please make sure to include as much information as possible along with your submission to help our taxonomy staff place the new species in our taxonomic database. Revised May 21, 1996 |
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