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Guide to NCBI resources Accession numbers For manuscript citation BankIt Sequin SequinMacroSend Upload .sqn files directly TBL2ASN Command line program Special submissions Genomes, batch sequences, alignments Whole Genome Shotgun Sequence submissions Third Party Annotation TPA database Transcriptome Shotgun Assembly TSA database Bacterial Genome Submission guidelines Sending data To GenBank Updates Make corrections, add annotations ESTs, STSs and GSSs Batch submission HTGS records High throughput genome sequences SNPs and other polymorphism data dbSNP submissions Confidentiality Withhold release |
BankIt: Submitting Via the WWWNCBI has developed a WWW form, called BankIt, for convenient and quick submission of sequence data.BankIt allows you to enter sequence information into a form, edit as necessary, and add biological annotation (e.g., coding regions, mRNA features). BankIt transforms your data into GenBank format for your review and when your record is completed, it can be submitted directly to GenBank. You have the option of adding information by using text boxes to describe in your own words the source of the sequence and its biological features. The GenBank annotation staff reviews the submitted textual information, incorporates it into the appropriate structured fields, and returns the record by e-mail for your review. BankIt is compatible with Netscape clients for Unix, Macs, and PCs. In addition, Internet Explorer for the PC and Mac have successfully been used. Sequin: Stand-alone Software for the Mac, PC/Windows, and UNIXIf you do not have access to the WWW, NCBI introduces a stand-alone submission program called Sequin.Sequin is an interactive, graphically-oriented program based on screen forms and controlled vocabularies that guides you through the process of entering your sequence and providing biological and bibliographic annotation. Sequin is designed to simplify the sequence submission process and to provide graphical viewing and editing options. It incorporates robust error checking and accommodates very long sequences and complex annotations. SequinMacroSendThis tool was designed for uploading large .sqn files directly to GenBank rather than sending large email attachments from stand-alone Sequin. Simply fill in the information on the SequinMacroSend form, upload the .sqn file, and the submission will be sent directly to the GenBank submission staff.TBL2ASNTbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank using many of the same functions as Sequin. It is used primarily for submission of complete genomes and large batches of sequences.Special Submissions: Genomes, Batch Sequences, AlignmentsSequin can be used for the submission of individual or small numbers of sequences. However, it was also designed to facilitate special types of submissions, and should be used instead of BankIt for the following types of submissions: genomes and other very long sequences; multiple sequences such as batch submissions and segmented sets, and population/phylogenetic/mutation studies.When preparing the submission of a genome, you can import the complete genome sequence into Sequin as well as a file containing the amino acid translations in FASTA format, if available. Sequin will automatically annotate the coding regions intervals based on the translations, and you can use Sequin to make further complex annotations. Sequin can also accept feature annotations in tab-delineated tables. Since the final submission file (*.sqn) will be quite large, please send it to the GenBank staff via FTP rather than by e-mail. To request a temporary FTP directory, please contact genomes@ncbi.nlm.nih.gov. When preparing a submission that contains multiple sequences, you can import a single file containing all the sequences in FASTA format, or as alignments in FASTA+GAP, PHYLIP, or NEXUS format. In addition, for population/phylogenetic/mutation studies, you can annotate one sequence and propagate the features onto the other sequences. When you complete the submission and select the 'prepare submission' option in the 'File' menu, Sequin will prepare a single *.sqn file that contains all the sequences. Send the *.sqn file by e-mail to: gb-sub@ncbi.nlm.nih.gov . If you are submitting two or more Sequin files, each of which contains multiple sequences, send each *.sqn file in a separate e-mail message. Please refer to the Sequin Quick Guide and documentation for additional information, both of which are accessible from the Sequin Web page. Whole Genome Shotgun Sequence SubmissionsNCBI is accepting contig assemblies from ongoing Whole Genome Shotgun (WGS) sequencing projects. These assemblies can contain annotations and should be updated as sequencing progresses and new assemblies are computed. Detailed submission instructions can be found on the WGS page.Third Party Annotation DatabaseThe TPA (Third Party Annotation) database, created by GenBank and its international partners DDBJ and EBI, accepts third party annotation of genomic sequences or computationally derived/assembled sequences. TPA submissions must use sequence data that is already represented in GenBank, and the analysis upon which the annotations are based must appear in a peer-reviewed scientific journal. Those wishing to add feature annotation, such as a gene or coding region, to an unannotated genomic sequence or wanting to combine two or more records to create a longer transcript sequence, can submit their analysis or assembly to the TPA database.Transcriptome Shotgun Assembly DatabaseTSA is an archive of computationally assembled sequences from primary data submitted to dbEST, the Short Read Archive (SRA), or the Trace Archive. The overlapping sequence reads from a complete transcriptome are assembled into transcripts by computational methods instead of by traditional cloning and sequencing of cloned cDNAs. The primary sequence data used in the assemblies and the assemblies must be submitted by the same submitter. TSA sequence records differ from EST and GenBank records because there are no physical counterparts to the assemblies asserted in the TSA record.Bacterial Genome Submission GuidelinesThe Bacterial Genome Submission Guidelines page provides a detailed guide to help bacterial genome submitters prepare their submissions using Sequin, an NCBI software tool for submitting and updating GenBank entries.Sending the Data to GenBankWhen using BankIt, the prepared sequence entries are submitted directly to GenBank through the WWW.When using Sequin, the output files for direct submission should be sent to GenBank by electronic mail to: gb-sub@ncbi.nlm.nih.gov or by uploading files to SequinMacroSend UpdatesNCBI processes update requests as well as new submissions. You can provide additional annotation, correct errors or omissions, or request the release of your "hold-until-published" record. BankIt or Sequin may be used for updates, or you can request changes as text in the body of an e-mail message. Be sure to give the accession number of the sequence to be updated along with all update information. Send it to:update@ncbi.nlm.nih.gov Submitters of a record maintain editorial control of that record. Any third party update information will be forwarded to the submitters of the record for review. Changes will be made to the record only at the submitters' request. If submitters can no longer be contacted, GenBank reserves the right to edit an entry to agree with the information presented in the original publication(s) cited in the entry. Submission of ESTs, STSs and GSSsBatches of ESTs (expressed sequence tags), STSs (sequence tagged sites), and GSSs (genome survey sequences) can be submitted via special streamlined procedures.Submission of HTGS RecordsThe NCBI has developed a protocol for high throughput genome sequencing centers to use when they submit large genomic records (usually Cosmids or BACs). Specialized tools, including fa2htgs and a "genome center version" of Sequin, have been created to help such centers produce these submission files in a convenient way. The HTG page not only provides detailed submission instructions to genome centers, but also informs GenBank users how to access the HTG sequences.Submission of SNPs and Other Polymorphism DataData on genetic variation in humans and other organisms can be submitted to the NCBI Database of Single Nucleotide Polymorphisms (dbSNP). Entries include single nucleotide polymorphisms (SNPs), small-scale insertion/deletions, polymorphic repetitive elements, and microsatellite variation. dbSNP is a separate resource from the GenBank database, and submissions do not receive GenBank accessions as noted above. However, dbSNP entries do receive dbSNP identifiers and contain links to associated GenBank records. Further information can be found on the dbSNP Submission page.ConfidentialitySome authors are concerned that the appearance of their data in GenBank prior to publication will compromise their work. GenBank will, upon request, withhold release of new submissions for a specified period of time. However, if a paper citing the sequence or accession number is published prior to the specified date, your sequence will be released upon publication.In order to prevent the delay in the appearance of published sequence data, we urge authors to inform us of the appearance of the published data. As soon as it is available, please send the full publication data--all authors, title, journal, volume, pages and date--to the following address: update@ncbi.nlm.nih.gov PrivacyIf you are submitting human sequences to GenBank, do not include any data that could reveal the personal identity of the source. It is our assumption that you have received any necessary informed consent authorizations that your organizations require prior to submitting your sequences.Revised February 18, 2009. |