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Sequin Entrez BLAST OMIM Taxonomy Structure

 

  1. Network-aware Sequin
  2. Sequin downloading issues
  3. Required organism information
  4. Adding modifiers to biological source information
  5. Problems importing sequences
  6. Alignment with previously submitted sequence(s)
  7. Importing annotation
  8. Annotation on sets
  9. Number signs in text in record viewer
  10. Export versus Save

  1. How do I change between the stand-alone and network-aware modes of Sequin?
  2. 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.

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  3. Why can't I download Sequin via ftp?
  4. 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.

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  5. What information is required regarding the source organism?
  6. 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 or you are submitting multiple sequences from the same organism, please include a strain, clone, isolate or other identifying information to differentiate this organism from others in the database. Commonly used source qualifiers include:

    [1] strain: If the sequence was obtained from a cultured isolate, then a strain identifier is required. (A strain identifier is not the same as a species epithet. The proper species name of your bacterial isolate is not required.) A strain may be designated in any manner: by the name of an individual or locality, or by a string of numbers and/or letters. For example, how do you distinguish this culture in your laboratory notebook?

    [2] clone: If this sequence was obtained by direct PCR-amplification and cloning, then please provide the name of the clone or laboratory identifier.

    [3] collection: If these organisms have been deposited in a culture collection, herbarium, or personal collection, please provide the collection number as either culture collection, specimen voucher, or biomaterial.

    [4] isolate: unique designation for those sequences which are isolated, but are not strains; commonly used for non-bacterial/non-archeal submissions. These can also be the laboratory designation that is used to distinguish your samples.

    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.

    If you are submitting sequence from a virus, please include strain or isolate, country where virus was collected, collection date, host, and serotype or genotype, if applicable.

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  7. 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?
  8. 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

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  9. I've formatted my sequence as you suggest, but I can't import it into Sequin. What could be wrong?
  10. If there is no line break (carriage return) between the definition line and the first line of sequence, you will not be able to import the sequence. Some word processors will break a single line into two lines without actually adding a carriage return. In this case, although the definition line and sequence will appear to be on two different lines, they really are on a single line. If you are unsure whether there is a carriage return, you can either set up your word processor so that it shows invisible characters such as carriage returns, or view the file in a text editor that does not create artificial line breaks.

    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.

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  11. How do I include an existing GenBank sequence in my alignment?
  12. 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.

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  13. How do I add annotation to my record in the record viewer?
  14. 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.

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  15. 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?
  16. 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.

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  17. Why do number signs appear within the text of my submission in the record viewer?
  18. 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.

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  19. What is the difference between the Export and Save functions under the Sequin File menu?
  20. 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.

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Questions or Comments?
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Revised November 24, 2008.