Network-aware Sequin

Network aware Sequin

Sequin

Entrez

BLAST

Most 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 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. Once this record is open in Sequin, its sequence can be updated in the Sequence Editor, or its annotations can be modified in the appropriate forms. The record can then be resubmitted to GenBank as a sequence update.

You can update only those records that 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 CDD Blast search

In Sequin's network-aware mode, users may perform a CDD Blast, which allows a search of the selected sequence against the NCBI's Conserved Domain Database .

Performing a PubMed look-up

In its network-aware mode, Sequin contains a built-in function that will look up the title, authors, and journal sections of a PubMed record if certain minimal information is 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), PubMed Unique Identifier (PMID), 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 or PMID. Without a MUID or PMID, the PubMed look-up cannot be performed.

Performing a Taxonomy look-up

A taxonomy look-up 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 look-ups are performed through the NCBI's Taxonomy database. If the taxonomy look-up 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.

Using the NCBI Desktop

The NCBI DeskTop is a window that directly displays the internal structure of the record being viewed in Sequin. It is meant only for advanced users and is described further in the Sequin Quick Guide.

Questions or Comments?
Write to the NCBI Service Desk

Revised June 10, 2004.