Current Affairs

What is Gen Bank? Gen Bank Submission Types? How to submit data to Gen Bank

What is Gen Bank?

GenBank is the NIH genetic sequence an annotated collection of all publicly available DNA sequences (Nucleic Acids Research, 201 Jan41(D1:D36-42). Gen Bank is part of the International Nucleotide Sequence Database collaboration which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NcBI. The three organizations exchange data on a daily basis.
The complete release notes for the current version of Gen Bank are available on the NCBI ftp site. A new release is made every two months. GenBank growth statistics for both the traditional GenBank divisions and the WGS division are available from each release.
An annotated sample GenBank record for a Saccharomyces cerevisiae gene demonstrates many of the features of the GenBank flat file format.

Access to GenBank
There are several ways to search and retrieve data from GenBank.
  • • Search GenBank for sequence identifiers and annotations with Entrez Nucleotide, which is divided into three divisions CoreNucleotde (the main collection), dbEST (Expressed Sequence Tags), and dbGSS (Genome Survey Sequences).
  • • Search and align GenBank sequences to a query sequence using BLAST (Basic Local Alignment Search Tool). BLAST searches Core Nucleotide, dbEST, and dbGSS independently, see BLAST info for more information about the numerous BLAST databases.
  • • Search, link, and download sequences programatically using NCBI e-utilities


GenBank Data Usage
The GenBank database is designed to provide and encourage access within the scientific community to the most up to date and comprehensive DNA sequence information. Therefore, NCBI places no restrictions on the use or distribution of the GenBank data. However, some submitters may claim patent, copyright, or other intellectual property rights in all or a portion of the data they have submitted. NcBI is not in a position to assess the validity of such claims, and therefore cannot provide comment or unrestricted permission concerning the use, copying, or distribution of the information contained in Gen Bank

Confidentiality
Some authors are concerned that the appearance of their data in Gen Bank prior to publication will
compromise their work. Gen Bank will, upon request, withhold release of new submissions for a specified period of time. A date must be specified; we can not hold a sequence indefinitely pending publication. However, if a paper citing the sequence or accession number is published prior to the specified date, the 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
authors, title, journal, volume, pages and date-to the following address update@ncbi.nlm.nih.gov

Privacy
If you are submitting human sequences to Gen Bank, do not include any data that could reveal the personal identity of the source Gen Bank assumes that the submitter has received any necessary informed consent authorizations required prior to submitting sequences.

Gen Bank Submission Types

Standard
GenBank accepts mRNA or genomic sequence data directly determined by the submitter The submission must include information about the source organism and annotation provided by the submitter. More details about adding annotation and sample files can be found in the Gen Bank Submissions Handbook. If you have any questions about the best method for submitting your data please contact our user services group at info@ncbi nlm.nih.gov.


The following data is not accepted by GenBank:
  • • Non contiguous sequences
  • • Primer sequences
  • • Protein sequences with no underlying nucleotide submission
  • • Sequence containing a mix of genomic and mRNA sequence
  • • Sequences without a physical counterpart (consensus sequences)
  • • Sequences with length less than 200 nucleotides

Raw sequence reads from next generation sequencing platforms should be submitted to the Sequence Read Archiv (SRA)
Sequence data not directly obtained by the submitter may be acceptable for the Third Party Annotation database


EST, STS, GSS
Batches of ESTs (expressed sequence tags) and GSSs (genome survey sequences) can be submitted via special streamlined procedures


High-Throughput Genomic (HTGs) Sequences
clone-based High-Throughput Genomic sequence (usually cosmids or BACs) submissions can be generated using tbl asn or Sequin The HTGs page provides detailed submission instructions for genome centers



Complete Microbial Genomes
The Bacteria Genome Submission Guidelines page provides a detailed guide to help bacteria genome submitters prepare their submissions using Sequin or tbl2asn



Whole Genome shotgun (WGs) sequences
Genomic sequence read-overfap contig sequences and assemblies from ongoing Whole Genome Shotgun MNGs) sequencing projects of prokaryotic and eukaryotic genomes with or without annotations can be submitted and should be updated as sequencing progresses and new assemblies are computed. Detailed submission instructions can be found on the WGS submission guide


Transcriptome shotgun Assembly ITSA) Sequences
Transcriptomic sequence read overlap contig sequences computationally assembled from primary data submitted to doEST the Seauence Read Archive usRA), or the Traca hive can be submitted to TSA Detailed submission instructions can be found on the TSA submission guide


Third Party Annotation (TPA)
The TPA Third Party Annotation) database accepts third party annotation of genomic sequences or computationally derived/assembled sequences TPA submissions must include sequence data that is already represented in Gen Bank, and the analysis upon which the annotations are based must appear in a peer-reviewed scientific journal. Detailed requirements and submission instructions can be found on the IPA submission guide


How to submit data to Gen Bank
The most important source of new data for Gen Bank is direct submissions from scientists. Gen Bank depends on its contributors to help keep the database as comprehensive, current. and accurate as possible NCBl 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 require DNA and amino acid sequences that are cited in articles be submitted to a public sequence repository (DDBJEMBL/Genbank INSDC) as part of the publication process. Data exchange between DDBJ, EMBL and GenBank occurs daily so 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. Sequence data submitted in advance of publication can be kept confidential if requested. Gen Bank will provide accession numbers for submitted sequences, usually within two working days. This accession number serves as an identifier for your submitted your data, and allows the community to retrieve the sequence 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


Submissions to Gen Bank
There are several options for submitting data to GenBank
• Bankit, a WWW-based submission tool with wizards to guide the submission process
• Sequin, NCBI’s stand-alone submission tool with wizards to guide the submission process is available by FTP for use on for MAC, PC, and UNIX platforms tbl2asn, a command-line prdgram, 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 and is available by FTP for use on MAC, PC and Unix platforms
• Submission Portal, a unified system for multiple submission types currently only 16s ribosomal RNA from uncultured bacterialarchaea can be submitted with the Gen Bank component of this tool. This will be expanded in the future to include other types of GenBank submissions. Genome and Transcriptome Assemblies can be submitted through the WGs and TSA portals, respectively.
• Barcode submission Tool, a www.based tool for the submission of sequences and trace read data for Barcode of Life projects based on the COI gene
Bankit, submission Portal and Barcode submission Tool are automatically submitted to Gen Bank submissions made with sequin or tbl2asn must be mailed to gb-sub@ncbi.nlm.nih.gov
Large files which may be truncated during mailing with conventional mail tools should be submitted directly using Seguin MacroSend
You can subscribe  be notified of updates to the submission tools
There are specialized, streamlined procedures for batch submissions of sequences such as EST and GSS sequences.


Submissions of Raw Sequence Reads
• Reads of Sanger-style sequencing can be submitted to the Trace Archae
• Runs of next-generation sequencing, for example from 454 or llumina can be submitted to the Sequence Read Archive
(SRA).



Updating or Revising a Gen Bank Sequence
Revisions or updates to Gen Bank entries can be made by the submitters at any time Information about the correct format for different types of updates can be found on the Update guidelines page Send updates and revisions
to gb-admin@ncbi.nlm.nih.gov Be sure to include the accession number of the sequence to be updated in the subject line.


Confidentiality
Some authors are concerned that the appearance of their data in Gen Bank prior to publication will compromise their work. Gen Bank 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 appearance of published sequence data, we urge authors to inform us of the appearance in the  of the published data. As soon as it is available, please send t full publication data authors, title, journal, volume, pages and date-to the following address update@ncbi.nlm.nih.gov


Privacy
If you are submitting human sequences to Gen Bank, do not include any data that could reveal the you are submitting human any necessary informed personal identity of the source. It is our assumption that you have received
consent authorizations that your organizations require prior to submitting your sequences.

About the author

Mallikarjuna

Leave a Comment

error: Content is protected !!