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The GenBank Submissions Handbook [Internet]. Bethesda (MD): National Center for Biotechnology Information (US); 2011-.

  • This publication is provided for historical reference only and the information may be out of date.

This publication is provided for historical reference only and the information may be out of date.

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The GenBank Submissions Handbook [Internet].

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Submitting Multiple Sequences as a Set

Created: ; Last Update: November 3, 2014.

Estimated reading time: 2 minutes

What is the difference between a batch and a set?

A Set is a group of sequences of the same gene and/or locus that are part of a population, mutation, phylogenetic or environmental study, and are published together in the same journal article. The sequences in a Set will be processed together as a unit and will be accessible together using Entrez PopSet.

A Batch is a group of sequences that are related in some way, but from different genes and/or loci, such as coming from the ame organism or being published together in the same journal article.

When can multiple sequences be submitted together as a set?

  • Members of a sequence set are published together in the same journal article, and are used to analyze the relatedness of a (sequence) population by analysis of the same gene or locus.
  • Below is a list of standard set types submitted to GenBank:
    • Population study:
      a set of sequences that were derived by sequencing the same gene from different isolates of the same organism.
    • Phylogenetic study:
      a set of sequences that were derived by sequencing the same gene from different organisms.
    • Mutation study:
      a set of sequences that were derived by sequencing multiple mutations of a single gene.
    • Environmental samples:
      a set of sequences that were derived by sequencing the same gene from a population of unclassified or unknown organisms.

In all the cases listed above, each sequence set is handled as a single submission, but each sequence submitted in a set will receive its own Accession number, and can be annotated independently.

Sequence sets can be submitted to GenBank via Sequin or BankIt.

How do I submit multiple sequences as a set?

To submit a group of sequences as a set, do the following:

  • Sequin:
    1.

    Fill out the Sequin Submitting Authors form.

    2.

    Select the set type on the Sequence Format Form (see the answer to “When can multiple sequences be submitted together as a set?).

    3.

    Sequin will prompt you to enter the data appropriate to the set.

  • BankIt:

    Once you have completed steps 1 (Contact) and 2 (Reference) of the BankIt submission process, step 3 (Submission Type) will give you a choice as to the submission type you intend to submit:
    1.

    If you intend to submit a set, select the radio button in front of “Set”.

    2.

    A question asking the number of sets you intend to submit will appear as will a list of set types (population/phylogenetic/mutation/environmental).

    3.

    Enter the total number of sets you intend to submit. (Note: you can only send one set per BankIt submission, so you will have to open a BankIt submission session for each additional set you intend to submit.).

    4.

    Select the radio button in front of the set type you intend to submit.

    5.

    From this point, BankIt will ask you for appropriate source and feature data for the set type you wish to submit.

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