Search sequences on the website

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transition-colors duration-150 ease-in-out font-bold">Search sequences on the website</a></li></ul></li></ul></div></nav></astro-island> <div class="mdContainer mdContainerItself text-gray-700 leading-relaxed"> <h1>Search sequences on the website</h1> <h2 id="mutations">Mutations</h2> <h3 id="nucleotide-mutations-and-insertions">Nucleotide mutations and insertions</h3> <p>A nucleotide mutation has the format <code><position><base></code> or <code><base_ref><position><base></code>. A <code><base></code> can be one of the four nucleotides <code>A</code>, <code>T</code>, <code>C</code>, and <code>G</code>. It can also be <code>-</code> for deletion and <code>N</code> for unknown. For example if the reference sequence is <code>A</code> at position 23 both: <code>23T</code> and <code>A23T</code> will yield the same results.</p> <p>If your organism is multi-segmented you must append the name of the segment to the start of the mutation, e.g. <code>S:23T</code> and <code>S:A23T</code> for a mutation in segment <code>S</code>.</p> <p>Insertions can be searched for in the same manner, they just need to have <code>ins_</code> appended to the start of the mutation. Example <code>ins_10462:A</code> or if the organism is multi-segmented <code>ins_S:10462:A</code>.</p> <h3 id="amino-acid-mutations-and-insertions">Amino acid mutations and insertions</h3> <p>An amino acid mutation has the format <code><gene>:<position><base></code> of <code><gene>:<base_ref><position><base></code>. A <code><base></code> can be one of the 20 amino acid codes. It can also be <code>-</code> for deletion and <code>X</code> for unknown. Example: <code>E:57Q</code>.</p> <p>Insertions can be searched for in the same manner, they just need to have <code>ins_</code> appended to the start of the mutation. Example <code>ins_NS4B:31:N</code>.</p> <h3 id="insertion-wildcards">Insertion wildcards</h3> <p>Loculus supports insertion queries that contain wildcards <code>?</code>. For example <code>ins_S:214:?EP?</code> will match all cases where segment <code>S</code> has an insertion of <code>EP</code> between the positions 214 and 215 but also an insertion of other AAs which include the <code>EP</code>, e.g. the insertion <code>EPE</code> will be matched.</p> <p>You can also use wildcards to match any insertion at a given position. For example <code>ins_S:214:?:</code> will match any (but at least one) insertion between the positions 214 and 215.</p> <h3 id="multiple-mutations">Multiple mutations</h3> <p>Multiple mutation filters can be provided by adding one mutation after the other.</p> <h3 id="any-mutation">Any mutation</h3> <p>To filter for any mutation at a given position you can omit the <code><base></code>.</p> <h3 id="no-mutation">No mutation</h3> <p>You can write a <code>.</code> for the <code><base></code> to filter for sequences for which it is confirmed that no mutation occurred, i.e. has the same base as the reference genome at the specified position.</p> <div class="text-right text-sm text-gray-500"> <a href="https://github.com/pathoplexus/pathoplexus/edit/main/monorepo/website/src/pages/docs/how-to/search-sequences-website.mdx" target="_blank" rel="noopener noreferrer" class="!text-gray-500 hover:!text-gray-800 !no-underline"> <svg viewBox="0 0 24 24" width="1.2em" height="1.2em" class="inline-block w-4 h-4 mr-1"><path fill="currentColor" d="M12 2A10 10 0 0 0 2 12c0 4.42 2.87 8.17 6.84 9.5c.5.08.66-.23.66-.5v-1.69c-2.77.6-3.36-1.34-3.36-1.34c-.46-1.16-1.11-1.47-1.11-1.47c-.91-.62.07-.6.07-.6c1 .07 1.53 1.03 1.53 1.03c.87 1.52 2.34 1.07 2.91.83c.09-.65.35-1.09.63-1.34c-2.22-.25-4.55-1.11-4.55-4.92c0-1.11.38-2 1.03-2.71c-.1-.25-.45-1.29.1-2.64c0 0 .84-.27 2.75 1.02c.79-.22 1.65-.33 2.5-.33s1.71.11 2.5.33c1.91-1.29 2.75-1.02 2.75-1.02c.55 1.35.2 2.39.1 2.64c.65.71 1.03 1.6 1.03 2.71c0 3.82-2.34 4.66-4.57 4.91c.36.31.69.92.69 1.85V21c0 .27.16.59.67.5C19.14 20.16 22 16.42 22 12A10 10 0 0 0 12 2"></path></svg> Edit this page </a> </div> </div> </div> </div> <hr class="border-t border-gray-1000"> <footer class="hidden sm:flex sm:z-6 sm:z-6 flex justify-between items-center h-20"> <div class="flex gap-5"> <a href="/api-documentation" class="text-gray-600"> API docs </a><a href="/about/governance" class="text-gray-600"> Governance </a><a href="/contact" class="text-gray-600"> Contact </a><a href="https://status.pathoplexus.org/" class="text-gray-600"> Status </a> </div> <a href="https://github.com/pathoplexus/pathoplexus" class="h-full py-6"> <img src="/github-mark.svg" class="h-full object-scale-down" alt="github-icon"> </a> </footer> </div> </body></html>

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Search sequences on the website | Pathoplexus