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seed-pos: skip region with gaps
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shenwei356 committed Aug 10, 2024
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62 changes: 39 additions & 23 deletions faqs/index.html
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<meta name="generator" content="Hugo 0.131.0">


<meta name="description" content="Does LexicMap support short reads? LexicMap is mainly designed for sequence alignment with a small number of queries (gene/plasmid/virus/phage sequences) longer than 200 bp by default. However, short queries can also be aligned.
If you just want to search long (&gt;1kb) queries for highy similar (&gt;95%) targets, you can build an index with a bigger -D/--seed-max-desert (200 by default), e.g.,
--seed-max-desert 450 --seed-in-desert-dist 150 Bigger values decrease the search sensitivity for distant targets, speed up the indexing speed, decrease the indexing memory occupation and decrease the index size." />
<meta name="description" content="Table of contents Table of contents Does LexicMap support short reads? Does LexicMap support fungi genomes? How&rsquo;s the hardware requirement? Can I extract the matched sequences? How can I extract the upstream and downstream flanking sequences of matched regions? Why isn&rsquo;t the pident 100% when aligning with a sequence from the reference genomes? Why is LexicMap slow for batch searching? Does LexicMap support short reads? LexicMap is mainly designed for sequence alignment with a small number of queries (gene/plasmid/virus/phage sequences) longer than 200 bp by default." />

<title>FAQs | LexicMap: efficient sequence alignment against millions of prokaryotic genomes​</title>

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content="FAQs"
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<meta property="og:site_name" content="LexicMap: efficient sequence alignment against millions of prokaryotic genomes\u200b" />
<meta property="og:description" content="Does LexicMap support short reads? LexicMap is mainly designed for sequence alignment with a small number of queries (gene/plasmid/virus/phage sequences) longer than 200 bp by default. However, short queries can also be aligned.
If you just want to search long (&gt;1kb) queries for highy similar (&gt;95%) targets, you can build an index with a bigger -D/--seed-max-desert (200 by default), e.g.,
--seed-max-desert 450 --seed-in-desert-dist 150 Bigger values decrease the search sensitivity for distant targets, speed up the indexing speed, decrease the indexing memory occupation and decrease the index size." />
<meta property="og:description" content="Table of contents Table of contents Does LexicMap support short reads? Does LexicMap support fungi genomes? How’s the hardware requirement? Can I extract the matched sequences? How can I extract the upstream and downstream flanking sequences of matched regions? Why isn’t the pident 100% when aligning with a sequence from the reference genomes? Why is LexicMap slow for batch searching? Does LexicMap support short reads? LexicMap is mainly designed for sequence alignment with a small number of queries (gene/plasmid/virus/phage sequences) longer than 200 bp by default." />
<meta property="og:type" content="article" />
<meta property="og:url" content="https://bioinf.shenwei.me/LexicMap/faqs/" />

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<meta name="twitter:card" content="summary" />
<meta name="twitter:title" content="FAQs" />
<meta name="twitter:description" content="Does LexicMap support short reads? LexicMap is mainly designed for sequence alignment with a small number of queries (gene/plasmid/virus/phage sequences) longer than 200 bp by default. However, short queries can also be aligned.
If you just want to search long (&gt;1kb) queries for highy similar (&gt;95%) targets, you can build an index with a bigger -D/--seed-max-desert (200 by default), e.g.,
--seed-max-desert 450 --seed-in-desert-dist 150 Bigger values decrease the search sensitivity for distant targets, speed up the indexing speed, decrease the indexing memory occupation and decrease the index size." />
<meta name="twitter:description" content="Table of contents Table of contents Does LexicMap support short reads? Does LexicMap support fungi genomes? How’s the hardware requirement? Can I extract the matched sequences? How can I extract the upstream and downstream flanking sequences of matched regions? Why isn’t the pident 100% when aligning with a sequence from the reference genomes? Why is LexicMap slow for batch searching? Does LexicMap support short reads? LexicMap is mainly designed for sequence alignment with a small number of queries (gene/plasmid/virus/phage sequences) longer than 200 bp by default." />


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"description": "Does LexicMap support short reads? LexicMap is mainly designed for sequence alignment with a small number of queries (gene\/plasmid\/virus\/phage sequences) longer than 200 bp by default. However, short queries can also be aligned.\nIf you just want to search long (\u003e1kb) queries for highy similar (\u003e95%) targets, you can build an index with a bigger -D\/--seed-max-desert (200 by default), e.g.,\n--seed-max-desert 450 --seed-in-desert-dist 150 Bigger values decrease the search sensitivity for distant targets, speed up the indexing speed, decrease the indexing memory occupation and decrease the index size.",
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"description": "Table of contents Table of contents Does LexicMap support short reads? Does LexicMap support fungi genomes? How’s the hardware requirement? Can I extract the matched sequences? How can I extract the upstream and downstream flanking sequences of matched regions? Why isn’t the pident 100% when aligning with a sequence from the reference genomes? Why is LexicMap slow for batch searching? Does LexicMap support short reads? LexicMap is mainly designed for sequence alignment with a small number of queries (gene\/plasmid\/virus\/phage sequences) longer than 200 bp by default.",
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Expand Down Expand Up @@ -1416,10 +1410,32 @@ <h2>More</h2>
>
<h1>FAQs</h1>
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<li><a href="#table-of-contents">Table of contents</a></li>
<li><a href="#does-lexicmap-support-short-reads">Does LexicMap support short reads?</a></li>
<li><a href="#does-lexicmap-support-fungi-genomes">Does LexicMap support fungi genomes?</a></li>
<li><a href="#hows-the-hardware-requirement">How&rsquo;s the hardware requirement?</a></li>
<li><a href="#can-i-extract-the-matched-sequences">Can I extract the matched sequences?</a></li>
<li><a href="#how-can-i-extract-the-upstream-and-downstream-flanking-sequences-of-matched-regions">How can I extract the upstream and downstream flanking sequences of matched regions?</a></li>
<li><a href="#why-isnt-the-pident-100-when-aligning-with-a-sequence-from-the-reference-genomes">Why isn&rsquo;t the pident 100% when aligning with a sequence from the reference genomes?</a></li>
<li><a href="#why-is-lexicmap-slow-for-batch-searching">Why is LexicMap slow for batch searching?</a></li>
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Does LexicMap support short reads?
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speed, decrease the indexing memory occupation and decrease the index size. While the
alignment speed is almost not affected.</p>
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<p>as we concatenate contigs with 1000-bp intervals of N’s to reduce the sequence scale to index.</p>
<p>For big and complex genomes, like the human genome (chr1 is ~248 Mb) which has many repetitive sequences, LexicMap would be slow to align.</p>
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<h3 id="hows-the-hardware-requirement"
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How&rsquo;s the hardware requirement?
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>hardware requirement</a>.</li>
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<h3 id="can-i-extract-the-matched-sequences"
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Can I extract the matched sequences?
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can extract subsequencess via genome ID, sequence ID and positions.
So you can use these information from the search result and expand the region positions to extract flanking sequences.</p>
<div class="flex align-center gdoc-page__anchorwrap">
<h3 id="why-isnt-the-pident-100-when-aligning-with-a-sequence-from-the-reference-genomes"
<h2 id="why-isnt-the-pident-100-when-aligning-with-a-sequence-from-the-reference-genomes"
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Why isn&rsquo;t the pident 100% when aligning with a sequence from the reference genomes?
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</h2>
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In the indexing step, all degenerate bases are converted to their lexicographic first bases. E.g., <code>N</code> is converted to <code>A</code>.
While for the query sequences, we don&rsquo;t convert them.</p>
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Why is LexicMap slow for batch searching?
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2 changes: 1 addition & 1 deletion search/en.data.min.json
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