1639 lines
26 KiB
HTML
1639 lines
26 KiB
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DNA Patterns
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#
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DNA patterns are useful for describing short DNA sequences like oligonucleotides. They are used by several OBITools
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like
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obimultiplex
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,
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obipcr
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or
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obigrep
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. The advantage of using DNA patterns over classical regular expressions is that they can be matched with errors. Allowed errors can be simple mismatches, or mismatches and insertions/deletions.">
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<meta property="og:description" content="DNA Patterns # DNA patterns are useful for describing short DNA sequences like oligonucleotides. They are used by several OBITools like obimultiplex , obipcr or obigrep . The advantage of using DNA patterns over classical regular expressions is that they can be matched with errors. Allowed errors can be simple mismatches, or mismatches and insertions/deletions.">
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<a href="/obidoc/obitools/obimatrix/" class="">obimatrix</a>
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<a href="/obidoc/obitools/obiuniq/" class="">obiuniq</a>
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<a href="/obidoc/obitools/obimultiplex/" class="">obimultiplex</a>
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<a href="/obidoc/obitools/obitagpcr/" class="">obitagpcr</a>
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<input type="checkbox" id="section-aa98fedd067b51150db59691a8ea8edd" class="toggle" />
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<label for="section-aa98fedd067b51150db59691a8ea8edd" class="flex justify-between">
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<a role="button" class="">Sequence alignments</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/obitools/obiclean/" class="">obiclean</a>
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<ul>
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</ul>
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</li>
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<label for="section-7433746525d8c2b29b033f765c869acd" class="flex justify-between">
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<a href="/obidoc/obitools/obipairing/" class="">obipairing</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/docs/commands/alignments/obipairing/fasta-like/" class="">The FASTA-like alignment</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/commands/alignments/obipairing/exact-alignment/" class="">Exact alignment</a>
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<ul>
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</ul>
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</li>
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</ul>
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<li>
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<a href="/obidoc/obitools/obipcr/" class="">obipcr</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/obitools/obirefidx/" class="">obirefidx</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/obitools/obitag/" class="">obitag</a>
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<ul>
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</ul>
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</li>
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<label for="section-5746f699d10490780dec8e30ab2dd3ce" class="flex justify-between">
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<a role="button" class="">Taxonomy</a>
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</label>
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<ul>
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<li>
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<a href="/obidoc/obitools/obitaxonomy/" class="">obitaxonomy</a>
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<ul>
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</ul>
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</li>
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<label for="section-3f50c4fe7ab436a56ae92897d5444956" class="flex justify-between">
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<a role="button" class="">Advanced tools</a>
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<li>
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<a href="/obidoc/obitools/obiscript/" class="">obiscript</a>
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<ul>
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</ul>
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<a role="button" class="">Others</a>
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<li>
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<a href="/obidoc/obitools/obimicrosat/" class="">obimicrosat</a>
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<ul>
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</ul>
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<a role="button" class="">Experimentals</a>
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<ul>
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<li>
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<a href="/obidoc/obitools/obicleandb/" class="">obicleandb</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obiconsensus/" class="">obiconsensus</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/obitools/obilandmark/" class="">obilandmark</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/docs/commands/tags/" class="">Glossary of tags</a>
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</li>
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</ul>
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</li>
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<input type="checkbox" id="section-9b1bcd52530c59dc4819b1f61c128f54" class="toggle" />
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<label for="section-9b1bcd52530c59dc4819b1f61c128f54" class="flex justify-between">
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<a role="button" class="">Cookbook</a>
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<li>
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<a href="/obidoc/docs/cookbook/illumina/" class="">Analysing an Illumina data set</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/cookbook/ecoprimers/" class="">Designing new barcodes</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/cookbook/local_genbank/" class="">Prepare a local copy of Genbank</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/docs/cookbook/reference_db/" class="">Build a reference database</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/docs/cookbook/minion/" class="">Oxford Nanopore data analysis</a>
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<ul>
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</ul>
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</li>
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</ul>
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</li>
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<li>
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<span>Programming OBITools</span>
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<ul>
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<li>
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<a href="/obidoc/docs/programming/expression/" class="">Expression language</a>
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<ul>
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</ul>
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<input type="checkbox" id="section-6d580829a667b5cca790b286d99a10fe" class="toggle" />
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<label for="section-6d580829a667b5cca790b286d99a10fe" class="flex justify-between">
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<a href="/obidoc/docs/programming/lua/" class="">Lua: for scripting OBITools</a>
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</label>
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<ul>
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<input type="checkbox" id="section-2fb081dac812d624eea5f4268fca9e26" class="toggle" />
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<label for="section-2fb081dac812d624eea5f4268fca9e26" class="flex justify-between">
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<a role="button" class="">Obitools Classes</a>
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</label>
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<a href="/obidoc/docs/programming/lua/obitools_classes/biosequence/" class="">BioSequence</a>
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<ul>
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</ul>
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<li>
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<a href="/obidoc/docs/programming/lua/obitools_classes/biosequenceslice/" class="">BioSequenceSlice</a>
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<ul>
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</ul>
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</li>
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<li>
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<a href="/obidoc/docs/programming/lua/obitools_classes/taxonomy/" class="">Taxonomy</a>
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<ul>
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<a href="/obidoc/docs/programming/lua/obitools_classes/taxon/" class="">Taxon</a>
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<ul>
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<a href="/obidoc/docs/programming/lua/obitools_classes/mutex/" class="">Mutex</a>
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<ul>
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</li>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
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</li>
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</ul>
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<script>(function(){var e=document.querySelector("aside .book-menu-content");addEventListener("beforeunload",function(){localStorage.setItem("menu.scrollTop",e.scrollTop)}),e.scrollTop=localStorage.getItem("menu.scrollTop")})()</script>
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<header class="book-header">
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<div class="flex align-center justify-between">
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<label for="menu-control">
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<img src="/obidoc/svg/menu.svg" class="book-icon" alt="Menu" />
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</label>
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<h3>DNA Patterns</h3>
|
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|
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<label for="toc-control">
|
|
|
|
<img src="/obidoc/svg/toc.svg" class="book-icon" alt="Table of Contents" />
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</label>
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</div>
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<aside class="hidden clearfix">
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<nav id="TableOfContents">
|
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<ul>
|
|
<li><a href="#dna-patterns">DNA Patterns</a>
|
|
<ul>
|
|
<li><a href="#syntax-of-a-dna-pattern">Syntax of a DNA Pattern</a></li>
|
|
<li><a href="#iupac-codes-for-ambiguous-bases">IUPAC Codes for Ambiguous Bases</a></li>
|
|
</ul>
|
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</li>
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</ul>
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</nav>
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</aside>
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</header>
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<article class="markdown book-article"><h1 id="dna-patterns">
|
|
DNA Patterns
|
|
<a class="anchor" href="#dna-patterns">#</a>
|
|
</h1>
|
|
<p>DNA patterns are useful for describing short DNA sequences like oligonucleotides. They are used by several <abbr title="A set of unix command line tools for manipulating DNA metabarcoding data">OBITools</abbr>
|
|
like <a href="http://metabar:8888/obidoc/obitools/obimultiplex/">
|
|
<abbr title="obimultiplex: "><code>obimultiplex</code></abbr>
|
|
</a>, <a href="http://metabar:8888/obidoc/obitools/obipcr/">
|
|
<abbr title="obipcr: the electronic PCR tool"><code>obipcr</code></abbr>
|
|
</a> or <a href="http://metabar:8888/obidoc/obitools/obigrep/">
|
|
<abbr title="obigrep: filter a sequence file"><code>obigrep</code></abbr>
|
|
</a>. The advantage of using DNA patterns over classical regular expressions is that they can be matched with errors. Allowed errors can be simple mismatches, or mismatches and insertions/deletions.</p>
|
|
<h2 id="syntax-of-a-dna-pattern">
|
|
Syntax of a DNA Pattern
|
|
<a class="anchor" href="#syntax-of-a-dna-pattern">#</a>
|
|
</h2>
|
|
<ul>
|
|
<li>Patterns are limited to sequences up to 63 bases long.</li>
|
|
<li>As all DNA sequences, they are represented from the 5’ end to the 3’ end.</li>
|
|
<li>Each base is represented by a single letter (A, C, G, T).</li>
|
|
<li>IUPAC codes can be used to represent ambiguous bases (N, M, K, R, Y, S, W, B, D, H, V, N, see table below).</li>
|
|
<li>Ambiguous positions can also be denoted by a range of base characters (<em>i.e.</em> <code>ATGC</code>) surrounded by square brackets (<code>[]</code>) : <code>[ATC]</code>.</li>
|
|
<li>A range of bases can negate by prefixing it with a <code>!</code> : <code>[!AC]</code>.</li>
|
|
<li>Patterns do not allow for ambiguity on the number of occurrences of a base.</li>
|
|
<li>Positions where errors are not allowed, are denoted by a sharp (<code>#</code>) symbol after the base.</li>
|
|
<li>Patterns are case unsensitive.</li>
|
|
</ul>
|
|
|
|
<link rel="stylesheet" href="/obidoc/css/vendors/admonitions.5c73bad2903e7d2d44ad118370ebd8c2cf5f239d4d93c283e55c00f2f8d30746.css" integrity="sha256-XHO60pA+fS1ErRGDcOvYws9fI51Nk8KD5VwA8vjTB0Y=" crossorigin="anonymous">
|
|
<div class="admonition example">
|
|
<div class="admonition-header"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 640 512"><path d="M192 96a48 48 0 1 0 0-96 48 48 0 1 0 0 96zm-8 384l0-128 16 0 0 128c0 17.7 14.3 32 32 32s32-14.3 32-32l0-288 56 0 64 0 16 0c17.7 0 32-14.3 32-32s-14.3-32-32-32l-16 0 0-64 192 0 0 192-192 0 0-32-64 0 0 48c0 26.5 21.5 48 48 48l224 0c26.5 0 48-21.5 48-48l0-224c0-26.5-21.5-48-48-48L368 0c-26.5 0-48 21.5-48 48l0 80-76.9 0-65.9 0c-33.7 0-64.9 17.7-82.3 46.6l-58.3 97c-9.1 15.1-4.2 34.8 10.9 43.9s34.8 4.2 43.9-10.9L120 256.9 120 480c0 17.7 14.3 32 32 32s32-14.3 32-32z"/></svg>
|
|
<span>Example</span>
|
|
</div>
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<div class="admonition-content">
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<p>A DNA pattern corresponding to the forward primer of the <em>Euka02</em> marker with no errors allowed
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at the two last bases on the 3’ end:</p>
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<p><code>TTTGTCTGSTTAATTSC#G#</code></p>
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</div>
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</div>
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<div class="admonition example">
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<div class="admonition-header"><svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 640 512"><path d="M192 96a48 48 0 1 0 0-96 48 48 0 1 0 0 96zm-8 384l0-128 16 0 0 128c0 17.7 14.3 32 32 32s32-14.3 32-32l0-288 56 0 64 0 16 0c17.7 0 32-14.3 32-32s-14.3-32-32-32l-16 0 0-64 192 0 0 192-192 0 0-32-64 0 0 48c0 26.5 21.5 48 48 48l224 0c26.5 0 48-21.5 48-48l0-224c0-26.5-21.5-48-48-48L368 0c-26.5 0-48 21.5-48 48l0 80-76.9 0-65.9 0c-33.7 0-64.9 17.7-82.3 46.6l-58.3 97c-9.1 15.1-4.2 34.8 10.9 43.9s34.8 4.2 43.9-10.9L120 256.9 120 480c0 17.7 14.3 32 32 32s32-14.3 32-32z"/></svg>
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<span>Example</span>
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</div>
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<div class="admonition-content">
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<p>The same pattern using base ranges for indicating the second <code>S</code> ambiguity:</p>
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<p><code>TTTGTCTGSTTAATT[CG]C#G#</code></p>
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</div>
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</div><h2 id="iupac-codes-for-ambiguous-bases">
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IUPAC Codes for Ambiguous Bases
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<a class="anchor" href="#iupac-codes-for-ambiguous-bases">#</a>
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</h2>
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<table border="1">
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<caption>
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IUPAC DNA ambiguity codes
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</caption>
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<tbody><tr align="center">
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<th>Symbol</th><th>Bases</th><th>Origin of designation</th></tr>
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<tr align="center"><td>G</td><td>G</td><td>Guanine</td></tr>
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<tr align="center"><td>A</td><td>A</td><td>Adenine</td></tr>
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<tr align="center"><td>T</td><td>T</td><td>Thymine</td></tr>
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<tr align="center"><td>C</td><td>C</td><td>Cytosine</td></tr>
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<tr align="center"><td>R</td><td>G or A</td><td>puRine</td></tr>
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<tr align="center"><td>Y</td><td>T or C</td><td>pYrimidine</td></tr>
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<tr align="center"><td>M</td><td>A or C</td><td>aMino</td></tr>
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<tr align="center"><td>K</td><td>G or T</td><td>Keto</td></tr>
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<tr align="center"><td>S</td><td>G or C</td><td>Strong interaction (3 H bonds)</td></tr>
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<tr align="center"><td>W</td><td>A or T</td><td>Weak interaction (2 H bonds)</td></tr>
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<tr align="center"><td>H</td><td>A or C or T</td><td>not-G, H follows G in the alphabet</td></tr>
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<tr align="center"><td>B</td><td>G or T or C</td><td>not-A, B follows A</td></tr>
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<tr align="center"><td>V</td><td>G or C or A</td><td>not-T (not-U), V follows U</td></tr>
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<tr align="center"><td>D</td><td>G or A or T</td><td>not-C, D follows C</td></tr>
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<tr align="center"><td>N</td><td>G or A or T or C</td><td>aNy</td></tr>
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</tbody>
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</table>
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</article>
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<script>(function(){function e(e){const t=window.getSelection(),n=document.createRange();n.selectNodeContents(e),t.removeAllRanges(),t.addRange(n)}document.querySelectorAll("pre code").forEach(t=>{t.addEventListener("click",function(){if(window.getSelection().toString())return;e(t.parentElement),navigator.clipboard&&navigator.clipboard.writeText(t.parentElement.textContent)})})})()</script>
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<li><a href="#dna-patterns">DNA Patterns</a>
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<li><a href="#syntax-of-a-dna-pattern">Syntax of a DNA Pattern</a></li>
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<li><a href="#iupac-codes-for-ambiguous-bases">IUPAC Codes for Ambiguous Bases</a></li>
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