Tag: Bankit

New wizard for submitting mRNA sequences to GenBank

New wizard for submitting mRNA sequences to GenBank

Do you submit eukaryotic nuclear mRNA sequences to GenBank? A new mRNA submission wizard is available! Built on the modern Submission Portal framework, this new wizard will bring you an enhanced experience, including:  

    • Guided submission experience specific for mRNA sequences 
    • Automated trimming of vector and removal of short sequences  
    • Easier input for source metadata 
    • New feature annotation web forms for coding region (CDS) and untranslated region (5’ UTR, 3’ UTR)  
    • Extensive feature previews (Figure 1) 
    • Faster sequence processing and accession assignment  
    • Access to a fix error workflow prior to accession assignment 

Watch a short video (4 min) to see how to annotate CDS features in this new wizard!  Continue reading “New wizard for submitting mRNA sequences to GenBank” →

Feature propagation in BankIt: easily annotate many sequences at once for GenBank submission

Do you need a quick way to annotate features on a similar set of sequences for your GenBank submission? You can now submit sequences from the same region or gene in an alignment format in BankIt and use the new ‘Feature propagation option’ (Figure 1) to apply features from a single sequence to other aligned sequences. You simply annotate one sequence and then copy that annotation across all the sequences in your submission.

Here’s how you can propagate features in three easy steps:

  1. Provide nucleotide sequences in an alignment format.
  2. Select a sequence and annotate it.
  3. Propagate the features and edit results.

Continue reading “Feature propagation in BankIt: easily annotate many sequences at once for GenBank submission” →

5 NCBI articles in 2018 Nucleic Acids Research database issue

5 NCBI articles in 2018 Nucleic Acids Research database issue

The 2018 Nucleic Acids Research database issue features several papers from NCBI staff that cover the status and future of databases including CCDS, ClinVar, GenBank and RefSeq. These papers are also available on PubMed. To read an article, click on the PMID number listed below.

Continue reading “5 NCBI articles in 2018 Nucleic Acids Research database issue” →

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” →