The Sequence Read Archive (SRA, previously known as the Short Read Archive) is a

bioinformatics Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combi ...

database that provides a public repository for

DNA sequencing DNA sequencing is the process of determining the nucleic acid sequence – the order of nucleotides in DNA. It includes any method or technology that is used to determine the order of the four bases: adenine, guanine, cytosine, and thymine. Th ...

data, especially the "short reads" generated by high-throughput sequencing, which are typically less than 1,000

base pairs A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA ...

in length. The archive is part of the

International Nucleotide Sequence Database Collaboration The International Nucleotide Sequence Database Collaboration (INSDC) consists of a joint effort to collect and disseminate databases containing DNA and RNA sequences. It involves the following computerized databases: DNA Data Bank of Japan (Japan) ...

(INSDC), and run as a collaboration between the NCBI, the European Bioinformatics Institute (EBI), and the DNA Data Bank of Japan (DDBJ). The archive was established by the National Center for Biotechnology Information (NCBI) in 2007 in order to provide a repository for data produced by

RNA-Seq RNA-Seq (named as an abbreviation of RNA sequencing) is a sequencing technique which uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment, analyzing the continuously changing c ...

and ChIP-Seq studies as well as large-scale studies including the Human Microbiome Project and the

1000 Genomes Project The 1000 Genomes Project (abbreviated as 1KGP), launched in January 2008, was an international research effort to establish by far the most detailed catalogue of human genetic variation. Scientists planned to sequence the genomes of at least one th ...

. Originally called the Short Read Archive, the name was changed in anticipation of future sequencing technologies being able to produce longer sequence reads. The volume of data deposited in the Sequence Read Archive has grown rapidly. As of September 2010, 65% of the SRA was human genomic sequence, with another 16% relating to human metagenome sequence reads. Much of this data was deposited through the 1000 Genomes Project. In June 2011, the data contained within the SRA passed 100 Terabases of DNA in volume. The preferred data format for files submitted to the SRA is the

BAM format SAMtools is a set of utilities for interacting with and post-processing short DNA sequence read alignments in the SAM (Sequence Alignment/Map), BAM (Binary Alignment/Map) and CRAM formats, written by Heng Li. These files are generated as output b ...

, which is capable of storing both aligned and unaligned reads. Internally the SRA relies on the NCBI SRA Toolkit, used at all three INSDC member databases, to provide flexible data compression, API access and conversion to other formats such as

FASTQ FASTQ format is a text-based format for storing both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. Both the sequence letter and quality score are each encoded with a single ASCII character for brevity. I ...

. NCBI announced their plan to close the NCBI SRA in February 2011 due to funding reduction. However, EBI and DDBJ announced that they would continue to support the SRA. In October 2011, NCBI announced continuation of funding for the SRA. Deposition of data in the SRA is mandated by most funding agencies and

open access journals Open access (OA) is a set of principles and a range of practices through which research outputs are distributed online, free of access charges or other barriers. With open access strictly defined (according to the 2001 definition), or libre op ...

. Nature Publishing Group journals require that DNA and RNA sequencing data is made available through the SRA.

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