Tag: sequin

Genome Workbench Submission Wizard to replace Sequin for prokaryotic and eukaryotic genome submissions in January 2021

If you use Sequin to submit prokaryotic or eukaryotic genome sequences to GenBank, you need to be aware that Sequin will be retired in January 2021. Genome Workbench’s Submission Wizard, which is already available for submitting annotated genomes, will be the submission tool to use for annotated genomes going forward.

Genome Workbench is desktop software that offers a rich set of integrated tools for studying and analyzing genetic data. You can explore and compare data from multiple sources, including the NCBI databases or the your own private data. The Submission Wizard, available since 2019, allows you to prepare submissions of single genomes where all sequences come from the same organism. This interface (Figure 1) is particularly valuable for:

  1. Eukaryotic genomes with annotations, for example those prepared with tbl2asn
  2. Prokaryotic genomes annotated by non-NCBI tools including Prokka and RAST.

Please register to attend our webinar on November 18 to see how to use Genome Workbench to prepare a submission. 

(Note: You should continue to submit organelle and viral genomes using BankIt. Please visit the Submission Portal page for information on other submission options.)

Figure 1. Genome Workbench and Submission Wizard. Once the Sequence Editing package is enabled the Submission menu can open the Genome Submission Wizard that prompts you to upload sequence data and presents  a tabbed set of forms for entering information about the submission. The Wizard validates the submission and provides editing capabilities for correcting errors. Continue reading “Genome Workbench Submission Wizard to replace Sequin for prokaryotic and eukaryotic genome submissions in January 2021”

How To Format Sequence Data For GenBank Submissions

Submitting sequences to GenBank can seem complicated at first, but starting with a solid foundation in the form of a properly formatted file will make the process go smoothly.

Before submitting sequence data to GenBank, the data must be formatted correctly, the most common file format being FASTA. This post will show you how to create a FASTA file for submitting single- and multiple-nucleotide sequences.

Submitters can upload FASTA-formatted sequence files using NCBI’s stand-alone software Sequin, command line tbl2asn or our web-based submission tool BankIt.

The image below depicts a single sequence in FASTA format. For multiple sequences, such as those of population or phylogenetic studies, environmental samples, and batch sequences of the same gene, create the file using the steps below and put the set of sequences together in a single FASTA file.

Image

Here is how to create the FASTA file:

Continue reading “How To Format Sequence Data For GenBank Submissions”