SITE MAP
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
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
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 Submitting Sequence Data to GenBank
The most important source of new data for GenBank® is direct submissions from scientists.
GenBank depends on its contributors to help keep the database as comprehensive, current,
and accurate as possible. NCBI provides timely and accurate processing and biological
review of new entries and updates to existing entries, and is ready to assist authors who
have new data to submit.
Receiving an
Accession
Number for your Manuscript
Most journals now expect that DNA and amino acid sequences that appear in articles will be submitted to a
sequence database before publication. Soon after submission, you will receive an accession number from the
database which you will be able to use in your article to refer to the sequence. Please be aware that it is
only necessary to submit the sequence to one database, whichever one is most convenient, without regard for
where the sequence may be published. Data exchange between GenBank, EMBL and DDBJ occurs daily. Sequence
data submitted in advance of publication can be kept confidential if requested.
Below are described various ways of submitting DNA sequences to GenBank. Essentially, there are two
principal ways, BankIt and Sequin. BankIt is a Web
submission tool and recommended for simple submissions. With BankIt you can indicate coding regions on an
mRNA along with a product and gene name. For more control over annotating your entry, segmented records,
or very long entries, Sequin, a stand-alone submission tool, is suggested.
GenBank will provide you with an accession number to identify your sequence, usually
within two working days, if the submission is received via electronic mail. This accession number serves as
confirmation that you have submitted your data, and allows the community to retrieve the data upon reading
the journal article.
The accession number should be included in your manuscript, preferably in a footnote
on the first page of the article, or as required by individual journal procedures.
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Submit now!!
Sequin
Stand-alone sequence submission tool
BankIt
For quick and simple submissions
VecScreen
Vector contamination screening tool
dbEST
dbGSS
dbSTS
Submit to GenBank divisions
GenBank
GenBank
Overview of the database
Search GenBank
Explore the data
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BankIt: Submitting Via the WWW
NCBI 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 UNIX
If 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.
SequinMacroSend
This 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.
TBL2ASN
Tbl2asn is a command-line program that automates the creation of sequence
records for submission to GenBank using many of the same functions as Sequin.
Special Submissions: Genomes, Batch
Sequences, Alignments
Sequin 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 Submissions
NCBI 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 Database
The 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 DDBJ/EMBL/GenBank, have annotation that is experimentlaly supported, and 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 as long as the provided annotation is supported by experimental evidence and published in a peer-reviewed journal.
Bacterial Genome Submission Guidelines
The 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 GenBank
When 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
As an alternative, the submission file can be copied to floppy disk and mailed to GenBank Submissions at:
GenBank Submissions
National Center for Biotechnology Information
National Library of Medicine
Bldg. 38A, Room 8N-803
Bethesda, MD 20894
Please label the disk with your name and file name and indicate whether it is a PC or MAC disk.
Updates
Revisions or updates to GenBank entries can be made at any time and can
be accepted as BankIt or Sequin files or as the text of an e-mail message. Click on the link for more information about updating information on GenBank records.
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 GSSs
Batches of ESTs (expressed sequence tags), STSs (sequence tagged sites), and GSSs (genome survey sequences) can be submitted via special streamlined procedures.
Submission of HTGS Records
The 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 Data
Data 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.
Confidentiality
Some 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
Privacy
If 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.
NOTE: The 'Authorin' submission tool and the E-mail submission
form were phased out on December 31, 1998, and submissions made with those tools are
no longer accepted as of that date. Instead, please use the improved submission
tools, BankIt and Sequin,
described above.
Disclaimer
Privacy statement
Revised December 4, 2003
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