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BankIt is a web-based GenBank submission tool that you should use to submit one or several sequences of the following kinds:

  • Protein-coding genes (complete or partial) from viruses, prokaryotes and eukaryotes (for example the mitochondrial cytochrome oxidase subunit I gene)
  • Other types of genes, including those sequenced as part of phylogenetic, population, or mutational studies/sets, except ribosomal RNA genes (rRNA) and internal transcribed spacer sequences (ITS)
  • Mobile elements, such as transposons and insertion sequences
  • Microsatellites and other genomic markers
  • Viral genomes (complete or partial), except Influenza and Norovirus
  • Phage genomes (complete or partial); unless you are also submitting the entire bacterial genome as a Complete genome submission or a Whole Genome Shotgun (WGS)
  • Mitochondrial, Chloroplast, or other Plastid genomes, (complete or partial) or genes from these organelles
  • Synthetic constructs, such as cloning and expression vectors
  • Third Party Annotation/Assembly sequences (TPA); allows you to submit your own annotation/assembly on publicly available sequences (GenBank primary sequences).  

GenBank considers the above listed sequence data as standard data. You can submit sequence data from next generation sequencing technologies using BankIt if they are assembled. Typically, you do not have to deposit raw reads, or register with BioProject/BioSample if you are submitting your sequences as a standard GenBank submission. See also the BankIt home page that lists data types that are not acceptable. 

A specialized tool, GenBank Submission Portal, is available for you if your data are of the following kinds:

  • Prokaryotic 16S ribosomal RNA, 23S ribosomal RNA, or 16S-23S ribosomal RNA intergenic spacer region
  • Eukaryotic nuclear small or large subunit ribosomal RNA, internal transcribed spacer 1 or 2, rRNA-ITS region
  • Mitochondrial or chloroplast small or large subunit ribosomal RNA
  • Metazoan COX1
  • Sequences of Influenza A, B, or C virus 
  • Norovirus sequences
  • Dengue sequences

In BankIt and Submission Portal you will complete all of the submission steps on the web.  Both tools accept sequence data in the FASTA format.  BankIt also accepts sequences in an alignment format (such as FASTA+GAP).

You can currently (January 2020) still use Sequin, a downloadable submission software. However, you should switch to BankIt becasue we are phasing out support for Sequin.