Search Raw Reads from NCBI’s SRA Database

We are thrilled to unveil an important addition to SequenceServer Cloud.

Our newest feature enables direct searching of raw reads from the NCBI’s Sequence Read Archive (SRA) database. This means you can search the stupendously large amounts of raw Illumina, Nanopore, Pacbio reads from each sample in every genomic and RNA-seq experiment. And also the smaller amounts from old Solexa and 454 runs.

This ability is critical for research questions that cannot be simply answered by examining assembled transcriptomes, genomes, or metagenomes, or by seeing summary counts of mapped reads.

As of March 19, 2024, this is in limited beta - contact support if you're interested in trialing this before its rolled out to all users.

How It Works

As outlined in the video above, it’s straightforward.

  1. Input Your Query: Paste your FASTA query sequence(s) into the search field.
  2. Select Your SRA Runs: Specify the identifiers of the SRA runs of interest.
  3. Specify RNA Analysis (If Applicable): For RNA-related searches, click “Allow spliced alignments”, so splicing isn’t penalized.
  4. Submit: Hit Submit. Each SRA is analyzed in parallel. This takes minutes to hours depending on data sizes involved (some SRA datasets are really big!)
  5. View Results: (see below)

Making Sense of SRA BLAST Analysis Results

Results appear progressively as analysis of each SRA run finishes. For each SRA sample, you get:

Potential Applications of SRA BLAST

We’re excited to see how SequenceServer Cloud users will use SRA BLAST. Likely applications include:

Happy Blasting!

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