Oct. 21, 2014
NCBI Sequin - Getting Started with
NCBI Sequin - Quick Guide http://www.ncbi.nlm.nih.gov/projects/Sequin/QuickGuide/sequin.htm
1. Start SEQUIN by typing 'sequin' at the command line. Or you can start SEQUIN through the BIRCH, and choose DNA --> Sequin - send annotated sequences to genbank.
2. Choose "Start new submission"
3. Fill in information in the Submission, Contact, Authors and Affiliation (all required). Make sure under submission, "tentative title for the manuscript" you fill in a title before proceeding . Follow towards the next form.
4. You will see a window entitled 'Sequence Format'. Continue with the default settings.
5. On the page entitled Nucleotide, click on "Import Nucleotide FASTA".
A new window will appear, and then import your .fsa file from the folder you saved it in.
6. By importing the .fsa file you will be able to Click on "Specify Topology". Set the topology to 'Circular'.
7. On the Organism page, click on the Add Organisms, Locations, and Genetic Codes.
A new window will appear and type in 'synthetic construct' under the heading Organism.
8. This is the minimum information needed to create a GenBank entry that can be used as a model for a restriction digest. Once the minimal information has been entered, follow the 'Next Page' links until a window pops up with the GenBank entry in it. (For other purposes, you may wish to annotate locations of coding sequences and other features of interest. In a laboratory setting, if you were planning to submit the sequence to GenBank, the most critical things to annotate for a construct such as this are the precise sources of the component sequences, in the FEATURES TABLE, along with a simple explanation in words in the DEFINITION line.)
9. To export your sequence to a GenBank file, choose File --> Export GenBank. Save your sequence as pBSGUS.gen.
A good introduction to SEQUIN, including screen shots, can be fund at http://www.ncbi.nlm.nih.gov/Sequin/.