Molecular Biology Data Sources: Sequence Data

• NCBI General Resources

Nucleotide Sequences

• GenBank
• Database of Short Genetic Variation (dbSNP)
• Database of Genomic Structural Variation (dbVar)
• Sequence Read Archive (SRA)

Amino Acid Sequences

• Protein

Access GenBank

What is it?

• Annotated collection of all publicly available DNA sequences
• Part of International Nucleotide Sequence Database Collaboration
• New release every 2 months

Access

• Public access
• NCBI places no restrictions on use or distribution of data
• Submitters may place patent, copyright or other intellectual property rights restrictions on all or a portion of data

How to Retrieve Data

• Search for sequence identifiers and annotations with Nucleotide
• Search and align sequences to query sequence with BLAST
• Search, link and download sequences using NCBI E-utilities
• Download sequence records in flat file format via FTP.  Full contents are described in the README.genbank file on GenBank's FTP server

Submissions

• Accepts mRNA or genomic sequence data determined directly by submitter
• Several options for submitting data to GenBank
• Will, upon request, withhold release of new submissions for specified period of time

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Access dbSNP

What is it?

• Archive and repository for short genetic variations, including:
  • Single nucleotide polymorphisms
  • Small-scale multi-base insertions or deletions
  • Short tandem repeats
• Integrates genetic variation and clinical data in collaboration with locus-specific databases and diagnostic laboratories
• Two major classes of content:
  • Submitted: original observations of sequence variation
  • Computed: generated during SNP build cycle
• Each entry includes:
  • Sequence surrounding polymorphism
  • Occurrence frequency of polymorphism
  • Experimental methods used to assay the variation

Access

•  Public access

How to Retrieve Data

• Searching
  • Where to start
    • dbSNP Homepage
    • Entrez
  • Multiple search options are available:
    • Visit dbSNP Access section of the new NCBI Handbook for more information
    • Use the SNP Advanced Search Builder page to construct a complex search using combinations of different search fields and qualifiers  (Advanced Search Builder video tutorial)
•  Data available for download via FTP from the dbSNP homepage

Submissions

• Accepts submissions from all organisms, including prokaryotes
• Loose definition of SNPs: no requirement about minimum allele frequencies
  • Large-scale insertions, deletions, etc. should be submitted to dbVar
• Need handle assignment from NCBI prior to submission
• For more information, visit Submissions to dbSNP

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Access dbVar

What is it?

• Database for large-scale genomic variants: insertions, deletions, translocations, inversions
• Accepts data from all species and clinical data

Access

• Public access

How to Retrieve Data

• Enter search terms into dbVar search box on homepage
  • Search will return studies and variants
  • Refine search using Limits or Advanced Search
  • For more information, visit dbVar Entrez Search Help
•  Data available via FTP on a per study and per assembly basis
  • For more information, visit dbVar FTP Site Help

Submissions

• Recommend submitting variant data > 50 base pairs to dbVar
• Accepts submissions from all organisms
• Accepts human clinical studies
• Complete information on how to submit data available on the dbVar homepage under "Submitting Data"

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Search Tools

• Entrez: NCBI's integrated database retrieval system that allows searching across 35 databases or within a single database
• Basic Local Alignment Search Tool (BLAST): Locates regions of similarity between biological sequences
  

Submission Information

• NCBI Submission Portal: NCBI's submission portal provides information on how to submit data to its databases, organized according to the type of data being submitted: sequence, project, biological materials, microarray, manuscript or clinical
  
• Submit Sequence Data to NCBI: Information on how to submit specific types of sequence data
  

Access SRA

What is it?

• Repository for raw sequencing data from next-generation sequencing technologies, including:
  • Roche 454 GS System®
  • Ion Torrent®
  • Illumina Genome Analyzer®
  • SOLiD®
  • Helicos HeliScope®
  • Complete Genomics®
• Goals for SRA
  • Provide central repository for next generation sequencing data
  • Provide links to other resources using this data
  • Provide retrieval based on ancillary information and sequence comparison
  • Track studies and experiments
  • Separate submission from content

Access

• Public access

How to Retrieve Data

• Searching
  • Where to start
    • SRA Homepage
    • Entrez
  • Multiple search options available, for more information, visit Searching for SRA Data
•  Multiple options for downloading data
  •  Via Aspera or FTP from SRA homepage
  • Run Browser
    • Download data from one or more runs in fasta and fastq form
    • Under "Browse" tab on SRA homepage
  • Individual level data will require controlled access to dbGaP
  • For more information, visit SRA Download Guide
• Using data
  • SRA Systems Development Kit provides Application Programming Interfaces for accession and manipulation of larger quantities of data
  • On SRA Homepage, under "Software"

Submissions

• Accepts primary sequencing data from next-generation sequencing platforms
• Submissions tools available under "Submit" tab on SRA homepage
• For more information, visit Submitting to the SRA

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Access Protein

What is it?

• Collection of protein sequences
• Source of sequences
  • GenPept sequences: translations of annotated coding regions in GenBank
  • RefSeq database: curated database of genomic DNA, transcripts (RNA) and protein products
  • Third Party Annotation (TPA) database: database of sequences derived from primary sequences
  • UniProtKB/Swiss-Prot
  • Protein Research Foundation
  • Protein Data Bank

Access

• Public access

How to Retrieve Data

• Searching
  • Enter keywords into search box on Protein homepage
    • Can limit search to records within a particular component database, gene location, publishing or modification date
  • Search and align sequences using BLAST
    • Select 'Protein BLAST' under Basic BLAST heading
  •  Additional tools available on Protein homepage
•  Multiple options available for downloading data
  • Download directly to file on computer by selecting 'Send To' in upper right hand corner of results page
  • Via FTP from:
    • GenBank
    • RefSeq
    • BLAST
    • Links to these resources found on Protein homepage

Submissions

• Protein sequences alone are not accepted, they must be accompanied by a nucleotide sequence (DNA or RNA), which can be submitted through GenBank
• For more information, please view the information in this guide on GenBank

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