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The FASTA sequence file format
#
The FASTA sequence file format is the most widely used sequence file format. This is probably due to its simplicity. It was originally created for the Lipman and Pearson
FASTA program
(
Citation: Pearson&#32;&amp;&#32;Lipman,&#32;1988
Pearson,&#32;
W.&#32;&amp;&#32;Lipman,&#32;
D.
&#32;
(1988).
&#32;Improved tools for biological sequence comparison.
Proceedings of the National Academy of Sciences of the United States of America,&#32;85(8).&#32;2444–2448.&#32;Retrieved from&#32;
http://www.ncbi.nlm.nih.gov/pubmed/3162770
)
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<meta property="og:description" content="The FASTA sequence file format # The FASTA sequence file format is the most widely used sequence file format. This is probably due to its simplicity. It was originally created for the Lipman and Pearson FASTA program ( Citation: Pearson &amp; Lipman, 1988 Pearson, W. &amp; Lipman, D. (1988). Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences of the United States of America, 85(8). 2444–2448. Retrieved from http://www.ncbi.nlm.nih.gov/pubmed/3162770 ) .">
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<h3>FASTA file format</h3>
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<article class="markdown book-article"><h1 id="the-fasta-sequence-file-format">
The <em>FASTA</em> sequence file format
<a class="anchor" href="#the-fasta-sequence-file-format">#</a>
</h1>
<p>The <em>FASTA</em> sequence file format is the most widely used sequence file format. This is probably due to its simplicity. It was originally created for the Lipman and Pearson
<a href="https://en.wikipedia.org/wiki/FASTA">FASTA program</a>
<span class="hugo-cite-intext"
itemprop="citation">(<span class="hugo-cite-group">
<a href="#pearson1988aa"><span class="visually-hidden">Citation: </span><span itemprop="author" itemscope itemtype="https://schema.org/Person"><meta itemprop="givenName" content="W R"><span itemprop="familyName">Pearson</span></span>&#32;&amp;&#32;<span itemprop="author" itemscope itemtype="https://schema.org/Person"><meta itemprop="givenName" content="D J"><span itemprop="familyName">Lipman</span></span>,&#32;<span itemprop="datePublished">1988</span></a><span class="hugo-cite-citation">
<span itemscope
itemtype="https://schema.org/Article"
data-type="article"><span itemprop="author" itemscope itemtype="https://schema.org/Person"><span itemprop="familyName">Pearson</span>,&#32;
<meta itemprop="givenName" content="W R" />
W.</span>&#32;&amp;&#32;<span itemprop="author" itemscope itemtype="https://schema.org/Person"><span itemprop="familyName">Lipman</span>,&#32;
<meta itemprop="givenName" content="D J" />
D.</span>
&#32;
(<span itemprop="datePublished">1988</span>).
&#32;<span itemprop="name">Improved tools for biological sequence comparison</span>.<i>
<span itemprop="about">Proceedings of the National Academy of Sciences of the United States of America</span>,&#32;85(8)</i>.&#32;<span itemprop="pagination">2444–2448</span>.&#32;Retrieved from&#32;
<a href="http://www.ncbi.nlm.nih.gov/pubmed/3162770"
itemprop="identifier"
itemtype="https://schema.org/URL">http://www.ncbi.nlm.nih.gov/pubmed/3162770</a></span>
</span></span>)</span>
.</p>
<p>In the <em>FASTA</em> format, a sequence is represented by a title line starting with a <strong>&gt;</strong> character, and the sequences themselves follow the
<a href="http://metabar:8888/obidoc/docs/patterns/dnagrep/#iupac-codes-for-ambiguous-bases"><code>iupac</code></a> code. The sequence is usually split into several other lines of the same length (expect for the last one). Several sequences can be stored in the same file. The first line of the next sequence also marks the end of the previous one.</p>
<pre tabindex="0"><code>&gt;my_sequence this is my pretty sequence
ACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGT
GTGCTGACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTACGTTGCAGTGTTT
AACGACGTTGCAGTACGTTGCAGT
</code></pre><p>The first word in the title line is the sequence identifier. The rest of the line is a description of the sequence. The <em>OBITools</em> extend this format by adding structured data to the title line. In the previous version of the <em>OBITools</em>, the structured data was stored after the sequence identifier in a <code>key=value;</code> format, as shown below. The sequence definition was stored as free text after the last <code>key=value;</code> pair.</p>
<a style="padding: 10px 20px; background-color: #cacaca; border: 1px solid #8e8080; border-bottom: none; border-radius: 5px 5px 0 0; box-shadow: 0 2px 5px rgba(0, 0, 0, 0.1)"
href="two_sequences_obi2.fasta" download="two_sequences_obi2.fasta">📄 two_sequences_obi2.fasta</a>
<DIV style="border: 2px solid #8e8080; border-radius: 0 0 5px 5px; padding: 20px; background-color: white; ">
<pre tabindex="0"><code class="language-fasta" data-lang="fasta">&gt;AB061527 obicleandb_level=family; count=1; family_name=Soricidae; genus_name=Sorex; genus_taxid=9379; obicleandb_trusted=2.2137847111025621e-13; species_name=Sorex unguiculatus; species_taxid=62275; taxid=62275; family_taxid=9376; Sorex unguiculatus mitochondrial NA, complete genome.
ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
agcttaaaactcaaaggacttggcggtgctttatatccct
&gt;AL355887 species_name=Homo sapiens; family_taxid=9604; genus_name=Homo; obicleandb_trusted=0; genus_taxid=9605; obicleandb_level=genus; species_taxid=9606; taxid=9606; count=2; family_name=Hominidae; Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.
ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
agcttaaaactcaaaggacctggcagttctttatatccct
</code></pre></td>
</DIV>
<p>With <em>OBITools4</em> a new format has been introduced to store structured data in the title line. The <em>key</em>/<em>value</em> annotation pairs are now formatted as a
<a href="https://en.wikipedia.org/wiki/JSON">JSON</a> map object. The definition is stored as an additional <em>key</em>/<em>value</em> pair using the <em>key</em> &lsquo;definition&rsquo;.</p>
<a style="padding: 10px 20px; background-color: #cacaca; border: 1px solid #8e8080; border-bottom: none; border-radius: 5px 5px 0 0; box-shadow: 0 2px 5px rgba(0, 0, 0, 0.1)"
href="two_sequences_obi4.fasta" download="two_sequences_obi4.fasta">📄 two_sequences_obi4.fasta</a>
<DIV style="border: 2px solid #8e8080; border-radius: 0 0 5px 5px; padding: 20px; background-color: white; ">
<pre tabindex="0"><code class="language-fasta" data-lang="fasta">&gt;AB061527 {&#34;count&#34;:1,&#34;definition&#34;:&#34;Sorex unguiculatus mitochondrial NA, complete genome.&#34;,&#34;family_name&#34;:&#34;Soricidae&#34;,&#34;family_taxid&#34;:9376,&#34;genus_name&#34;:&#34;Sorex&#34;,&#34;genus_taxid&#34;:9379,&#34;obicleandb_level&#34;:&#34;family&#34;,&#34;obicleandb_trusted&#34;:2.2137847111025621e-13,&#34;species_name&#34;:&#34;Sorex unguiculatus&#34;,&#34;species_taxid&#34;:62275,&#34;taxid&#34;:62275}
ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
agcttaaaactcaaaggacttggcggtgctttatatccct
&gt;AL355887 {&#34;count&#34;:2,&#34;definition&#34;:&#34;Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.&#34;,&#34;family_name&#34;:&#34;Hominidae&#34;,&#34;family_taxid&#34;:9604,&#34;genus_name&#34;:&#34;Homo&#34;,&#34;genus_taxid&#34;:9605,&#34;obicleandb_level&#34;:&#34;genus&#34;,&#34;obicleandb_trusted&#34;:0,&#34;species_name&#34;:&#34;Homo sapiens&#34;,&#34;species_taxid&#34;:9606,&#34;taxid&#34;:9606}
ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
agcttaaaactcaaaggacctggcagttctttatatccct
</code></pre></td>
</DIV>
<p>The <a href="http://metabar:8888/obidoc/obitools/obiconvert/">
<abbr title="obiconvert: convert format of a sequence file"><code>obiconvert</code></abbr>
</a> command, like all other <em>OBITools4</em> commands, has two options <code>--output-json-header</code> and <code>--output-OBI-header</code> to choose between the new
<a href="https://en.wikipedia.org/wiki/JSON">JSON</a> format and the old <em>OBITools</em> format. The <code>--output-OBI-header</code> option can be abbreviated to <code>-O</code>. By default, the new
<a href="https://en.wikipedia.org/wiki/JSON">JSON</a> <em>OBITools4</em> format is used, so only the <code>-O</code> option is really useful if the old format is required for compatibility with other software.</p>
<p>Converting from the new
<a href="https://en.wikipedia.org/wiki/JSON">JSON</a> format to the old <em>OBITools</em> format:</p>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>obiconvert -O two_sequences_obi4.fasta
</span></span></code></pre></div>
<pre tabindex="0"><code class="language-fasta" data-lang="fasta">&gt;AB061527 obicleandb_level=family; count=1; family_name=Soricidae; genus_name=Sorex; genus_taxid=9379; obicleandb_trusted=2.2137847111025621e-13; species_name=Sorex unguiculatus; species_taxid=62275; taxid=62275; family_taxid=9376; Sorex unguiculatus mitochondrial NA, complete genome.
ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
agcttaaaactcaaaggacttggcggtgctttatatccct
&gt;AL355887 species_name=Homo sapiens; family_taxid=9604; genus_name=Homo; obicleandb_trusted=0; genus_taxid=9605; obicleandb_level=genus; species_taxid=9606; taxid=9606; count=2; family_name=Hominidae; Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.
ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
agcttaaaactcaaaggacctggcagttctttatatccct
</code></pre></td>
<p>Converting from the old <em>OBITools</em> format to the new
<a href="https://en.wikipedia.org/wiki/JSON">JSON</a> format:</p>
<div class="highlight"><pre tabindex="0" style="color:#f8f8f2;background-color:#272822;-moz-tab-size:4;-o-tab-size:4;tab-size:4;"><code class="language-bash" data-lang="bash"><span style="display:flex;"><span>obiconvert two_sequences_obi2.fasta
</span></span></code></pre></div>
<pre tabindex="0"><code class="language-fasta" data-lang="fasta">&gt;AB061527 {&#34;count&#34;:1,&#34;definition&#34;:&#34;Sorex unguiculatus mitochondrial NA, complete genome.&#34;,&#34;family_name&#34;:&#34;Soricidae&#34;,&#34;family_taxid&#34;:9376,&#34;genus_name&#34;:&#34;Sorex&#34;,&#34;genus_taxid&#34;:9379,&#34;obicleandb_level&#34;:&#34;family&#34;,&#34;obicleandb_trusted&#34;:2.2137847111025621e-13,&#34;species_name&#34;:&#34;Sorex unguiculatus&#34;,&#34;species_taxid&#34;:62275,&#34;taxid&#34;:62275}
ttagccctaaacttaggtatttaatctaacaaaaatacccgtcagagaactactagcaat
agcttaaaactcaaaggacttggcggtgctttatatccct
&gt;AL355887 {&#34;count&#34;:2,&#34;definition&#34;:&#34;Human chromosome 14 NA sequence BAC R-179O11 of library RPCI-11 from chromosome 14 of Homo sapiens (Human)XXKW HTG.; HTGS_ACTIVFIN.&#34;,&#34;family_name&#34;:&#34;Hominidae&#34;,&#34;family_taxid&#34;:9604,&#34;genus_name&#34;:&#34;Homo&#34;,&#34;genus_taxid&#34;:9605,&#34;obicleandb_level&#34;:&#34;genus&#34;,&#34;obicleandb_trusted&#34;:0,&#34;species_name&#34;:&#34;Homo sapiens&#34;,&#34;species_taxid&#34;:9606,&#34;taxid&#34;:9606}
ttagccctaaactctagtagttacattaacaaaaccattcgtcagaatactacgagcaac
agcttaaaactcaaaggacctggcagttctttatatccct
</code></pre></td>
<p>The actual format of the header is automatically detected when <em>OBITools4</em> commands read a FASTA file.</p>
<h2 id="references">
References
<a class="anchor" href="#references">#</a>
</h2>
<section class="hugo-cite-bibliography">
<dl>
<div id="pearson1988aa">
<dt>
Pearson&#32;&amp;&#32;Lipman
(1988)</dt>
<dd>
<span itemscope
itemtype="https://schema.org/Article"
data-type="article"><span itemprop="author" itemscope itemtype="https://schema.org/Person"><span itemprop="familyName">Pearson</span>,&#32;
<meta itemprop="givenName" content="W R" />
W.</span>&#32;&amp;&#32;<span itemprop="author" itemscope itemtype="https://schema.org/Person"><span itemprop="familyName">Lipman</span>,&#32;
<meta itemprop="givenName" content="D J" />
D.</span>
&#32;
(<span itemprop="datePublished">1988</span>).
&#32;<span itemprop="name">Improved tools for biological sequence comparison</span>.<i>
<span itemprop="about">Proceedings of the National Academy of Sciences of the United States of America</span>,&#32;85(8)</i>.&#32;<span itemprop="pagination">2444–2448</span>.&#32;Retrieved from&#32;
<a href="http://www.ncbi.nlm.nih.gov/pubmed/3162770"
itemprop="identifier"
itemtype="https://schema.org/URL">http://www.ncbi.nlm.nih.gov/pubmed/3162770</a></span>
</dd>
</div>
</dl>
</section>
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<li><a href="#the-fasta-sequence-file-format">The <em>FASTA</em> sequence file format</a>
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