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COVID-19 Viral Genome Analysis Pipeline
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SARS-CoV-2 Sequence Locator

Purpose: To find the position of your nucleotide or protein sequence(s) relative to the appropriate viral reference strain; or to give you a sequence based on a coordinate location.

Find the location of a sequence
Sequence base type Nucleotide Amino acid
Paste your input here
or upload your file
Email results

-- OR --
Retrieve a region by its coordinates of reference sequences
Enter coordinates: from to (Enter '1' and 'end' to retrieve the entire region.)
Region
Retrieve Nucleotide or Amino acid output
include surrounding region

Details: This tool has many uses:

  • find the start and end coordinates of your input sequence(s), relative to the reference strains:
    • Genbank: Wuhan-Hu-1 NC_045512
    • GISAID: hCoV-19/Wuhan/WIV04/2019 | EPI_ISL_402124
  • show which genes or proteins your query touches,
  • show a graphical view of the location of your sequence(s) relative to the reference sequence,
  • display both the nucleotide sequence and protein translation of your input as it aligns to reference sequences,
  • retrieve a section of the reference sequences based on its coordinates.

last modified: Mon Jun 29 15:31 2020



GISAID data provided on this website is subject to GISAID's Terms and Conditions

Questions or comments? Contact us at seq-info@lanl.gov.

 
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