How do I change between the stand-alone and network-aware modes of Sequin?

There are two ways to change between the stand-alone and network-aware modes of Sequin. (1) When you launch the Sequin program, you will see a menu called Misc on the Welcome to Sequin form. Select Net Configure under this menu. (2) If you are already running Sequin, select the option under the record viewer Misc menu called Net Configure. In either case, Sequin will prompt you to set certain preferences and will then run a network configuration program. In most cases, the default preferences are sufficient. To switch Sequin back into its stand-alone mode, select the Net Configure option again. You must restart Sequin before any changes to the network mode take effect. For additional information, see the Sequin help documentation under Net Configure.

Why can't I download Sequin via ftp?

Try setting your browser to use passive ftp. Many organizations allow only passive ftp transfers through their firewalls. See Downloading with ftp for instructions on how to configure your browser for passive mode.

What information is required regarding the source organism?

For most organisms, the genus species designation is required. If the organism is currently listed in the Taxonomy Browser , you do not need to include information concerning its lineage in your submission. However, if the species is a new species not listed in the Taxonomy Browser, please include lineage information in a source note.

If the source organism has not been identified to the species level, please include a strain, clone, isolate or other identifying information to differentiate this organism from others in the database.

If you are submitting a sequence from mouse (Mus musculus) or rat (Rattus norvegicus), please include strain information.

If you are submitting sequence from a vouchered specimen, please include the specimen voucher.

I would like to add some additional information about the biological source from which the sequence is derived. What modifiers can I include, and how should I annotate them on the sequence?

A complete list of available source modifiers and information about their use is available. These modifiers can be included in the nucleotide FASTA definition lines used for submission.

Alternatively, Sequin can accept a tab-delimited table of source information during the submission process. Use the Import Source Modifiers button on the Organism page to import this table. The first column in the table must contain the Sequence Identifiers (SeqIDs) used in the FASTA definition lines and each subsequent column must contain a different source modifier. The first row in the table must contain the labels for each column. For example,

Seq_ID	country	collection-date	specimen-voucher
seq1	USA	13-May-2005	MVZ 186209	
seq2	Angola	26-Oct-2004	MNCN 11956	
seq3	Aruba	02-Apr-1998	SEL 92-038a living accession	

I've formatted my sequence as you suggest, but I can't import it into Sequin. What could be wrong?

Also note that you must use IUPAC nucleotide base codes in your nucleotide FASTA. Any other characters, including "?" or "-" will be removed from the sequence. Use the symbol "N" for ambiguous or unknown nucleotides.

How do I include an existing GenBank sequence in my alignment?

Sequin accepts the alignment formats FASTA+GAP, PHYLIP, MACAW, NEXUS interleaved, and NEXUS contiguous. In each of these formats you can include a previously submitted sequence within the alignment such that it will not receive a new accession number. To do t his, use a SeqID in the format accU12345, where U12345 is the Accession number of the pre-existing sequence. This sequence will app ear within the alignment but will not be treated as a new submission when processed.

How do I add annotation to my record in the record viewer?

You can add any single feature or descriptor using the lists in the Annotate Menu in the record viewer. Each menu choice will launch a feature or descriptor-specific editor, where you can add information about the descriptor or feature. You must input the nucleotide location of any feature on the Location subpage.

You can also import a five-column, tab-delimited table of features. The correct format for this table is outlined on a separate page. You import this file using Open under the File menu in the record viewer.

I have an alignment of multiple sequences. I would like to annotate the same feature (such as rRNA) on all the sequences. Is there an easy way to do this with Sequin?

In addition to using the table discussed above, you can add annotation to all members of a set in one of three ways.

1. You can add the same feature across the entire span of each sequence by using the Batch Feature option under the Annotate Menu in the record viewer. The feature must span the entire nucleotide sequence of each member, you can not annotate specific nucleotide locations using this option.
2. If you have included an alignment in your submission, you can propagate any annotated feature from one sequence to the other sequences using the Feature Propagate option under the Edit menu in the record viewer. For example, you can annotate a CDS feature on the first sequence in your set and use this function to annotate a similar CDS with locations based on the alignment to the other nucleotide sequences in the set.
3. If you have inlcuded an alignment in your submission, you can add annotation to each member of the set using the alignment coordinates in the Alignment Assistant.

Why do number signs appear within the text of my submission in the record viewer?

Sequin and the GenBank database can only display ASCII characters. We can not display special characters, such as Greek letters or those with an accent or an umlaut. Please edit your record to change the number sign which appears for non-ASCII characters to the correct ASCII character before submission to the database.

What is the difference between the Export and Save functions under the Sequin File menu?

The Sequin Save and Save As functions save the record so that it can be re-opened by Sequin. The record is saved in a format called ASN.1, a data description language used by the NCBI. Be sure to save the record before you exit Sequin or you will lose all of your work. The ASN.1 format is also the format into which the file is saved when you prepare your your record for submission (by clicking the Done button on the record viewer or selecting Prepare Submission under the File menu). The database staff use the ASN.1 to build your sequence submission.

The Sequin Export function exports the current view of the record for some views. The information that is exported depends on the option that is selected in the Display Format pop-up menu. In GenBank or EMBL display format, Sequin will export a copy of the record as it would appear in GenBank or EMBL format, respectively. In FASTA display format, Sequin will export the DNA sequence in FASTA format. In ASN.1 display format, Sequin will export a copy of the record in ASN.1. Sequin will not export the Sequence or Graphic view.

Note that Exporting the record is not the same as Saving. A file that has been created by Exporting cannot be re-opened by Sequin and should not be submitted to the database.